Electron protein

One of the key technologies required for fabricating biomolecular electronic devices concerns with molecular assembly of electronic proteins such as redox enzymes in monolayer scale on the electrode surface. Furthermore the molecularly assembled electronic proteins are required to be electronically communicated with the electrode. Individual protein molecules on the electrode surface should be electronically accessed through the electrode. 

Rusnak, F. and T. Reiter. 2000. Sensing electrons Protein phosphatase redox regulation. Tr. Biochem. Sci. 25 527-9. 

Mincer, J.S., Nunez, S. and Schwartz, S.D. (2004). Coupling protein dynamics to reaction center electron density in enzymes an electronic protein promoting vibration in human purine nucleoside phosphorylase. J. Theor. Comp. Chem. 3, 501-509... 

Coon, J.1(2009) Collisions or electrons Protein sequence analysis in the 21st century. Analytical Chemistry, 81, 3208-3215. 

This background is provided to show that work done in this laboratory initially on mediated electron protein studies led to the study of direct electron transfer reactions of proteins and enzyme at electrodes. It was a not a large intellectual step to consider direct studies of electron transfer proteins at electrodes, given this background and the work being done in other laboratories in the area of chemically modified electrodes at that time. Still, it was the unexpected that led to actually thinking that an electron transfer protein might react reversibly or quasi-reversibly at an elecflode, as will be described later. 

Birge, R.R. et al, Biomolecular electronics protein-based associative processors and volumetric memories. /. Phys. Chem. B., 1999,103 10746-10766. 

SAMs are generating attention for numerous potential uses ranging from chromatography [SO] to substrates for liquid crystal alignment [SI]. Most attention has been focused on future application as nonlinear optical devices [49] however, their use to control electron transfer at electrochemical surfaces has already been realized [S2], In addition, they provide ideal model surfaces for studies of protein adsorption [S3]. 

Protein adsorption has been studied with a variety of techniques such as ellipsome-try [107,108], ESCA [109], surface forces measurements [102], total internal reflection fluorescence (TIRE) [103,110], electron microscopy [111], and electrokinetic measurement of latex particles [112,113] and capillaries [114], The TIRE technique has recently been adapted to observe surface diffusion [106] and orientation [IIS] in adsorbed layers. These experiments point toward the significant influence of the protein-surface interaction on the adsorption characteristics [105,108,110]. A very important interaction is due to the hydrophobic interaction between parts of the protein and polymeric surfaces [18], although often electrostatic interactions are also influential [ 116]. Protein desorption can be affected by altering the pH [117] or by the introduction of a complexing agent [118]. 

Figure Bl.17.6. A protein complex (myosin SI decorated filamentous actin) embedded in a vitrified ice layer. Shown is a defociis series at (a) 580 mn, (b) 1130 mn, (c) 1700 mn and (d) 2600 mn underfocus. The pictures result from averagmg about 100 individual images from one electron micrograph the decorated filament length shown is 76.8 nm.

Figure Bl.17.11. Reconstructed density of an a,p-tiibulin protein dimer as obtained from electron crystallography (Nogales etal 1997). Note the appearance of the p-sheets ((a), marked B) and the a-helices ((b), marked H) in the density. In particular the right-handed a-helix H6 is very clear. Pictures by courtesy of E Nogales and Academic Press.

Apart from the sheer complexity of the static stmctures of biomolecules, they are also rather labile. On the one hand this means that especial consideration must be given to the fact (for example in electron microscopy) that samples have to be dried, possibly stained, and then measured in high vacuum, which may introduce artifacts into the observed images [5]. On the other, apart from the vexing question of whether a protein in a crystal has the same stmcture as one freely diffusing in solution, the static stmcture resulting from an x-ray diffraction experiment gives few clues to the molecular motions on which operation of an enzyme depends [6]. 

The spatial arrangement of atoms in two-dimensional protein arrays can be detennined using high-resolution transmission electron microscopy [20]. The measurements have to be carried out in high vacuum, but since tire metliod is used above all for investigating membrane proteins, it may be supposed tliat tire presence of tire lipid bilayer ensures tliat tire protein remains essentially in its native configuration. 

A salient feature of natural surfaces is tliat tliey are overwhelmingly electron donors [133]. This is tlie basis for tlie ubiquitous hydrophilic repulsion which ensures tliat a cell can function, since massive protein-protein aggregation and protein-membrane adsorjition is tliereby prevented. In fact, for biomolecule interactions under typical physiological conditions, i.e. aqueous solutions of moderately high ionic strengtli, tlie donor-acceptor energy dominates. 

Sensitivity levels more typical of kinetic studies are of the order of lO molecules cm . A schematic diagram of an apparatus for kinetic LIF measurements is shown in figure C3.I.8. A limitation of this approach is that only relative concentrations are easily measured, in contrast to absorjDtion measurements, which yield absolute concentrations. Another important limitation is that not all molecules have measurable fluorescence, as radiationless transitions can be the dominant decay route for electronic excitation in polyatomic molecules. However, the latter situation can also be an advantage in complex molecules, such as proteins, where a lack of background fluorescence allow s the selective introduction of fluorescent chromophores as probes for kinetic studies. (Tryptophan is the only strongly fluorescent amino acid naturally present in proteins, for instance.)... 

The pathway model makes a number of key predictions, including (a) a substantial role for hydrogen bond mediation of tunnelling, (b) a difference in mediation characteristics as a function of secondary and tertiary stmcture, (c) an intrinsically nonexponential decay of rate witlr distance, and (d) patlrway specific Trot and cold spots for electron transfer. These predictions have been tested extensively. The most systematic and critical tests are provided witlr mtlrenium-modified proteins, where a syntlretic ET active group cair be attached to the protein aird tire rate of ET via a specific medium stmcture cair be probed (figure C3.2.5). 

Figure C3.2.6. Zones associated witlr the distinctive decay of electronic coupling tlrrough a-helical against p-sheet stmctures in proteins. Points shown refer to specific rates in mtlrenium-modified proteins aird in tire photosyntlretic reaction centre. From Gray H B aird Wiirkler J R 1996 Electron trairsfer in proteins A . Rev. Biochem. 65 537.

The cross relation has proven valuable to estimate ET rates of interest from data tliat might be more readily available for individual reaction partners. Simple application of tire cross-relation is, of course, limited if tire electronic coupling interactions associated with tire self exchange processes are drastically different from tliose for tire cross reaction. This is a particular concern in protein/protein ET reactions where tire coupling may vary drastically as a function of docking geometry. 

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