Proteine, tridimensional structure

The membrane structure described by the model of Singer and Nicolspn (1) has the major advantages of considering three universal properties of membranes, i.e. the organization of lipids as a fluid bilayer, the penetration of proteins into the bilayer, and the a-S3rmmetry of the membrane components. This model as such is however too general and perhaps not accurate in the description of protein tridimensional structures in the bilayer. 

S Non-covalent Protein Complexes and Tridimensional Structural Information... 

Mass spectrometry also provides information on the tridimensional structure of proteins. Often, the information from mass spectrometry complements those obtained by other techniques such as circular dichroism, nuclear magnetic resonance or fluorescence. In some circumstances, mass spectrometry, by its speed and sensitivity, allows information to be obtained that is impossible to obtain by other techniques. 

Below here we will focus on an original computational method that accounts for the experimentally observed radioprotection of the partners in DNA-protein complexes. Validated by comparison between experiment and calculation, it can be used to predict the damage extent and distribution in any biomolecule or complex of biomolecules whose tridimensional structure is known. 

The RADACK (contraction of RADiation-induced attACK) model, that we have developed [9,10], accounts for the experimentally determined probabilities of radiolytic damages caused by the OH radical attack in all forms of DNA (B [11], Z [12], triplex [13], quadruplex [14]), in DNA-protein complexes [15] and has the potential to predict radiolytic attack probabilities in other molecules or assemblies. Direct ionisation effects are not taken into account. The determination of relative probabilities of reaction ofthe target with the OH radicals takes into account two factors 1) the accessibility of the reactive sites of the target since it uses the exact tridimensional structure of the macromolecule or assembly as determined by NMR, crystallography or as built up by molecular modelling, and 2) the chemical reactivity of the residues (nucleotides or amino-acids). 

In prokaryotes, most transcription factors belong to the Helix-Turn-Helix family (19). Proteins of this class typically form homodimers, whose tridimensional structure is symmetrical. As a consequence, many prokaryote transcription factors bind to spaced motifs (also called dyads), where each halfmotif is bound by one element of the homodimer. The width of the spacing between the two contact points is transcription factor-specific, and can vary from 0 to 20 nt. Because we are working with bacterial sequences, we will illustrate the pattern discovery step by using a tool dedicated to the detection of spaced motifs dyad-analysis (20) (see Note 9). 

Elucidation of distances between prosthetic groups in a complex and eventually of the complete tridimensional structure in the complex. Orientation and mobility of protein complexeses in the membrane. Orientation and the mobility of quinones (For example chemiosmotic coupling requires that quinones are reduced inside and reoxidized outside). 

Different isoforms of 15-lipoxygenase have been purified to homogeneity from mammalian sources, including reticulocytes and leukocytes, and complementary DNAs encoding them have been cloned. The reticulocyte 15-lipoxygenase is a cytosolic protein, whose amino acid sequence is 65% similar to human 5-lipoxygenase and 45% similar to type I soybean lipoxygenase (whose tridimensional structure has been resolved by... 

Here we discuss structures that have been established at the atomic level revealing the exact conformation of the polypeptide chain. All were determined by X-ray diffraction analysis of a tridimensional protein crystal. Some o -helical membrane protein structures have been analyzed by electron diffraction of o-dimensional crystals, although generally with a lower accuracy. For a long time structural analyses by NMR... 

Proteins are basically formed from one or more chains of polypeptides (with a particular primary structure). The chains of amino acids in proteins, being very long, can coil and fold. This spatial arrangement of amino acids is described by the secondary and tertiary structures of proteins. The arrangement of the amino acids that are near one another in the linear sequence is described by the secondary structure. For example, the amino acids may generate a helical structure (a-helix) such that the amino acids chain forms a tridimensional rod, and the amino acids that are four units apart can have hydrogen bonds between their N-H and C=0 groups. An example of a stereo view of an a-helix... 

Structural unit of these lattices can be the atom - for the rare gases, the proper molecule, i.e., the finite molecule for elementary substances of type S3, P4, Xj (X= I, Cl, F, Br), or of binary compounds from class CH, CI, etc., infinite associations of atoms - linear (Se, Te), flat (graphite) or tridimensional (globular proteins). 

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