Protein two-dimensional

Wattiez R et al. Human bronchoalveolar lavage fluid protein two-dimensional database study of interstitial lung diseases. Electrophoresis 2000 21 2703-2712. Yanagida M et al. Matrix assisted laser desorption/ionization-time of flight-mass spectrometry analysis of proteins detected by anti-phosphotyrosine antibody on two-dimensional-gels of fibrolast cell lysates after tumor necrosis factor-alpha stimulation. Electrophoresis 2000 21 1890-1898. 

Wattiez R et al. Human bronchoalveolar lavage fluid protein two-dimensional database study of interstitial lung diseases. Electrophoresis 2000 21 2703-2712. 

Fountoulakis, M., Schuller, E., Hardmeier, R., Bemdt, P. and Lubec, G. (1999) Rat brain proteins two-dimensional protein database and variations in the expression level. Electrophoresis 20, 3572-3579. 

The high-resolution and the high scaling factor of 2D PISEMA, for the first time, enabled the use of the dipolar dimension to resolve resonances from non-selectively or uniformly labeled proteins. Three-Dimensional experiments were used to enhance the resolution of resonances from uniformly N-labeled peptides and proteins embedded in lipid bilayers. This was successfully demonstrated on aligned samples containing uniformly N-labeled membrane-associated peptides and proteins. Two-dimensional PISEMA spectra of some of these systems showed limited resolution due to a small frequency dispersion of resonances from a-helices oriented on the surface of the bilayer in both N chemical shift and H- N dipolar coupling dimensions. However, when an additional H chemical shift dimension was invoked, the 3D H chemical shift/ H- N dipolar coupling/ N chemical shift spectra of these systems considerably increased the resolution of peaks. ... 

Walz T and Grigorieff N 1998 Eleotron orystallography of two-dimensional orystals of membrane proteins J. Struct. Biol. 121 142-61... 

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. 

Fig. 9. Two-dimensional sketch of the 3N-dimensional configuration space of a protein. Shown are two Cartesian coordinates, xi and X2, as well as two conformational coordinates (ci and C2), which have been derived by principle component analysis of an ensemble ( cloud of dots) generated by a conventional MD simulation, which approximates the configurational space density p in this region of configurational space. The width of the two Gaussians describe the size of the fluctuations along the configurational coordinates and are given by the eigenvalues Ai.

The amount of computation necessary to try many conformers can be greatly reduced if a portion of the structure is known. One way to determine a portion of the structure experimentally is to obtain some of the internuclear distances from two-dimensional NMR experiments, as predicted by the nuclear Over-hauser effect (NOE). Once a set of distances are determined, they can be used as constraints within a conformation search. This has been particularly effective for predicting protein structure since it is very difficult to obtain crystallographic structures of proteins. It is also possible to define distance constraints based on the average bond lengths and angles, if we assume these are fairly rigid while all conformations are accessible. 

Biological membranes provide the essential barrier between cells and the organelles of which cells are composed. Cellular membranes are complicated extensive biomolecular sheetlike structures, mostly fonned by lipid molecules held together by cooperative nonco-valent interactions. A membrane is not a static structure, but rather a complex dynamical two-dimensional liquid crystalline fluid mosaic of oriented proteins and lipids. A number of experimental approaches can be used to investigate and characterize biological membranes. However, the complexity of membranes is such that experimental data remain very difficult to interpret at the microscopic level. In recent years, computational studies of membranes based on detailed atomic models, as summarized in Chapter 21, have greatly increased the ability to interpret experimental data, yielding a much-improved picture of the structure and dynamics of lipid bilayers and the relationship of those properties to membrane function [21]. 

Two-dimensional crystals of membrane proteins can be studied by electron microscopy... 

Figure 12.3 Two-dimensional crystals of the protein bacteriorhodopsin were used to pioneer three-dimensional high-resolution structure determination from electron micrographs. An electron density map to 7 A resolution (a) was obtained and interpreted in terms of seven transmembrane helices (b).

The three-dimensional structure of the bacterial membrane protein, bac-teriorhodopsin, was the first to be obtained from electron microscopy of two-dimensional crystals. This method is now being successfully applied to several other membrane-bound proteins. 

Figure 18.17 Two-dimensional NMR spectnim of the C-terminal domain of a cellulase. The peaks along the diagonal correspond to the spectrum shown in Figure 18.16b. The off-diagonal peaks in this NOE spectrum represent interactions between hydrogen atoms that are closer than 5 A to each other in space. From such a spectrum one can obtain information on both the secondary and tertiary structures of the protein. (Courtesy of Per Kraulis, Uppsala.)...

Two-dimensional NMR spectra of proteins are interpreted by the method of sequential assignment... 

Wright, P. What can two-dimensional NMR tell us about proteins Trends Biochem. Sci. 14 255-260,... 

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