Topology of proteins

Maslov S, Sneppen K (2002). Specificity and stability in topology of protein networks. Science 296 910-913. 

Although this spectral approach has had but limited application thus far, it appears to have great promise for exploring the topology of proteins. 

Furthermore, the parameters derived from protein three-dimensional structures characterize the topology of proteins, which play an important role in kinetics of protein folding. 

In contrast to conformational disorders, experimental evidence of lipid effects on topology of protein membranes is lacking. However the existence of variations in lipid composition between different intracellular compartments... 

Immunological methods produce antibodies that will bind to target positions in the protein seqnence. " The target segment in the protein will bind antibodies if this segment is outside the membrane or if it is positioned only on one side of the membrane. From this basis one then attempts to reconstruct the topology of proteins. 

We have also shown how it is possible to obtain by the pref method (version 2.0) very reliable predictions for the stmcture and topology of proteins with unknown structural and topological features. With this we have demonstrated the usefulness of the development of such methods and especially the quality of the pref method which in many cases gives very reliable predictions and thus considerably shortens the time-consuming and expensive experimental research in the determination of membrane protein structures. 

Topology diagrams are useful for classification of protein structures... 

Koch, I., Kaden, R, Selbig, J. Analysis of protein sheet topologies by graph theoretical methods. Prot Struc. Func. Genet. 12 314-323, 1992. 

Richardson, J.S. p-sheet topology and the relatedness of proteins. Nature 268 495-500, 1977. 

Transmembrane Signaling. Figure 2 Membrane topology of receptors that are associated with effector proteins. Upon binding to their cognate ligands (cyan), receptor proteins without intramolecularly linked effector domain couple via transducer proteins (yellow) to or directly recruit and activate effector proteins (red). Notch receptors release their transducer domains upon proteolytic cleavage, a, p and y stand for G-protein a-, p- and y-subunits, respectively. 

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