Rotational proteins

In the Fi part, a hexameric a3/ 3 protein complex, the three //-units are catalyti-cally active. In a three-step process, conformational changes of the active site induce the binding of ADP and phosphate inside a pocket of the enzyme, followed by formation of the triphosphate from these reactants and subsequent release of the new ATP molecule from the active site. The conformational changes necessary for passage through this three-step cycle are caused by a bent, rotating protein axle in... 

See also Motions of Cilia and Flagella, Bacterial Motility - Rotating Proteins... 

Bacterial Motility Rotating Proteins (Figure 8.29, Figure 8.31)... 

ATP synthesis at Fj. In essence, the chemical energ) of the proton gradient is converted to mechanical energy in the form of the rotating proteins. This mechanical enei is then converted to the chemical energy stored in the high-enei phosphate bonds of ATP. 

For large molecules, such as proteins, the main method in use is a 2D technique, called NOESY (nuclear Overhauser effect spectroscopy). The basic experiment [33, 34] consists of tluee 90° pulses. The first pulse converts die longitudinal magnetizations for all protons, present at equilibrium, into transverse magnetizations which evolve diirhig the subsequent evolution time In this way, the transverse magnetization components for different protons become labelled by their resonance frequencies. The second 90° pulse rotates the magnetizations to the -z-direction. 

Other external forces or potentials can also be used, e.g., constant forces, or torques applied to parts of a protein to induce rotational motion of its domains (Wriggers and Schulten, 1997a). 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

The FAB source operates near room temperature, and ions of the substance of interest are lifted out from the matrix by a momentum-transfer process that deposits little excess of vibrational and rotational energy in the resulting quasi-molecular ion. Thus, a further advantage of FAB/LSIMS over many other methods of ionization lies in its gentle or mild treatment of thermally labile substances such as peptides, proteins, nucleosides, sugars, and so on, which can be ionized without degrading their. structures. 

To understand the function of a protein at the molecular level, it is important to know its three-dimensional stmcture. The diversity in protein stmcture, as in many other macromolecules, results from the flexibiUty of rotation about single bonds between atoms. Each peptide unit is planar, ie, oJ = 180°, and has two rotational degrees of freedom, specified by the torsion angles ( ) and /, along the polypeptide backbone. The number of torsion angles associated with the side chains, R, varies from residue to residue. The allowed conformations of a protein are those that avoid atomic coUisions between nonbonded atoms. 

Fats and, through the use of lignosiilfonic acid, proteins can be Rotated from the wastewaters of slaughterhouses and other food-processing installations [Hopwood, Jn.st. Chem. Eng. Symp. Ser, 41, Ml (1975)]. After further treatment, the floated sludge has been fed to swine. 

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