Protein orientations

NMR data [95]. This new method requires two sets of dipolar couplings from two different protein orientations. Together with the backbone dipolar couplings that are typically used (i.e., amide NH, C N, CaC, CaHa and the two-bond HNC ), CaCp dipolar couplings are also needed. Provided that the orientation of one peptide plane is known independently, the dipolar coupling data give rise to two possible orientations for the subsequent peptide plane, where the conformations about the alpha carbon in these two orientations are mirror images. One of the conformations can be ruled out because of chirality. 

The ability to sequence proteins at low levels and sometimes in a high throughput fashion has considerably advanced protein-oriented molecular biological research. The qualitative change affects the two criteria sensitivity and throughput. 

Electron transfer from Fe(II)cytc to ccp(ES) proceeds with a rate of 800 s at — AG° = 0.90 eV [73]. From measurements of ET rates at other driving forces, the cyt c/ccp reorganization energy was estimated to be 1.5 eV the relatively large X value may be a result of redox-dependent fluctuations of the protein-protein orientation, since the primary binding mode is electrostatic (salt bridges) [73]. 

The nse of self-assembled monolayers of proteins by direct chemical attachment of the peptide to a modified snrface obviates some of the protein orientation difficnlties observed in the construction of LB mono-layers. An initial report of the construction of peptide SAMs on silanized qnartz was pnblished in early 1998 (185). Pilloud et al. have utilized the covalent ligation of protein cysteine thiols to thiol-terminated silanized... 

Clearly a set of monoclonal antibodies may help elucidate the nature of adsorbed protein orientation and conformation. Such studies are in progress by several groups. 

It has often been assumed that the second step, intracomplex ET, takes place within a static reactant complex. However, a number of cases have been observed in which the reactant complex is not static, but undergoes dynamic configurational fluctuations (defined as protein-protein orientations in the bound complex) [65] or conformational changes (defined as a tertiary structure of each protein) [40]. If the reaction is rate limited by dynamic fluctuation in configuration rather than by the... 

McLean MA, Stayton PS, Sligar SG (1993) Engineering protein orientation at surfaces to control macromolecular recognition events. Anal Chem 65 2676-2678 Shen Z, Tan H, Zhang Y et al (2008) Engineering peptide linkers for scFv immunosensors. Anal Chem 80 1910-1917... 

Spin labeling Ligand or protein None Spin label for either ligand or protein Orientation, simultaneous binding 10 M0 M X y" ... 

In all the biomimetic membranes previously described and allowing the incorporation of proteins, the protein orientation in the membrane is purely casual. At most, if one of the two extremembrane domains of the protein is much bulkier than the other, incorporation in a tBLM occurs preferentially with the bulkier domain turned toward the aqueous phase, in view of the hmited spaciousness of the hydrophihc moiety of the tBLM. Moreover, the packing density of the reconstituted proteins in the hpid bilayer is not well controlled. The need for a well-defined protein orientation with respect to the electrode surface is particularly felt with redox membrane proteins, in which the electrons involved in a chain of redox couples are conveyed across the membrane in a weh-defined direction. 

Noto M, Keng D, Teraoka I et al (2007) Detection of protein orientation on the silica microsphere surface using transverse electric/transverse magnetic whispering gallery modes. Biophys J 92 4466-4472... 

Transition metal complexes of phthalocyanine encaged in faujasite type zeolites have been reported as efficient catalysts in the oxidation of alkanes at room temperature and atmospheric pressure [6-13]. These catalysts constitute potential inorganic mimics of remarkable enzymes such as monooxygenase cytochrome P-450 which displays the ultimate in substrate selectivity. In these enzymes the active site is the metal ion and the protein orientates the incoming substrate relative to the active metal center. Zeolites can be used as host lattices of metal complexes [14, 15]. The cavities of the aluminosilicate framework can replace the protein terciary structure of natural enzymes, thus sieving and orientating the substrate in its approach to the active site. Such catalysts are constructed by the so-called ship in a bottle synthesis the metal phthalocyanine complexes are synthesized in situ within the supercages of the zeolite... 

Lipid-anchored proteins are just one example of membrane proteins that are asymmetrically located with respect to the faces of cellular membranes. Each type of transmembrane protein also has a specific orientation with respect to the membrane faces. In particular, the same part(s) of a particular protein always faces the cytosol, whereas other parts face the exoplasmic space. This asymmetry in protein orientation confers different properties on the two membrane faces. (We describe how the orientation of different types of transmembrane proteins is established during their synthesis in Chapter 16.) Membrane proteins have never been observed to flip-flop across a membrane such movement, requiring a transient movement of hydrophilic amino acid residues through the hydrophobic interior of the membrane, would be energetically unfavorable. Accordingly, the asymmetry of a transmembrane protein, which is established during its biosynthesis and insertion into a membrane, is maintained throughout the protein s lifetime. 

Two other features of membrane structure illustrate its asymmetry. First, carbohydrates are always attached on the outside surface of the cell. Second, membrane protein orientation (flipping) does not occur, so that proteins always maintain the same polarity. 

Yasuda Y, Sugino H, Toyotama H et al. Control of protein orientation in molecular photoelectric devices using Langmuir-Blodgett films of photosynthetic reaction centers from Rhodopseudomonas viridis. Bioelectrochem Bioenerg 1994 34 135-139. 

The protein orientational averj ing in Eqs. (3), (5), (6), and (8) requires a transformation between laboratory-fixed and protein-fixed coordinates. The protein-fixed axes (abc) can be reoriented into the laboratory-fixed axes (jcyz) by applying a sequence of counterclockwise rotations through the independent Euler angles The first rotation is made through... 

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