Protein Structure and Topology

Jones, D., Taylor, W., and Thornton, J. (1994). A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33, 3038-3049. 

F. M. Marassi and S. J. Opella, A solid-state NMR index of helical membrane protein structure and topology. J. Magn. Reson.. 2000,144, 150-155. 

Recognition Approach to the Prediction of All-Helical Membrane Protein Structure and Topology. Available http //blolnf.cs.ucl.ac.uk/psipred/. 

Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res. 2005 15 385-392. 

E. M. Marassi, A simple approach to membrane protein secondary structure and topology based on NMR spectroscopy. Biophys. J., 2001, 80, 994—1003. 

D Correlation Spectroscopy. A simple, quahtative approach has been described for the determination of membrane protein secondary structure and topology in lipid bilayer membranes." The new approach is based on the observation of wheel-like resonance patterns in the NMR H- N/ N polarization inversion with spin exchange at the magic angle (PISEMA) and H/ N HETCOR spectra of membrane proteins in oriented lipid bilayers. These patterns, named Pisa wheels, have been previously shown to reflect helical wheel projections of residues that are characteristic of a-helices associated with membranes. This study extends the analysis of these patterns to P-strands associated with membranes and demonstrates that, as for the case of a-helices, Pisa wheels are extremely sensitive to the tilt, rotation, and twist of P-strands in the membrane and provide a sensitive, visually accessible, qualitative index of membrane protein secondary structure and topology. 

It has been shown that the secondary structure and topology of membrane proteins can be described by inspection of two-dimensional dipolar... 

MEMSAT [70] is a program for predicting the secondary structure and topology (helical orientation) of integral membrane proteins. 

Predictions for Proteins for Which, According to the SWISS-PROT Data Bank, Structure and Topology Are Not Known... 

It has been pointed out that the swiss-prot data bank includes a certain number of membrane proteins for which the structure is not quite reliably determined, in part because older methods were used to determine the location and number of transmembrane segments. These older methods are less reliable because they were trained on a smaller sets of proteins. Hence, we suggest that it is necessary to use new and better methods for detecting these defective topologies in order to carry out additional research on them with the aim to obtain their more accurate structures and topologies. In the present report we have shown one of possible ways to carry out such a procedure and this has been illustrated using several examples. In this we also used the positive inside rule, predictions on similar proteins, and predictions obtained by other methods. 

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. 

Mesleh MF, Lee S, Veglia G, Thiriot DS, Marassi FM, Opella SJ (2003) Dipolar waves map the structure and topology of helices in membrane proteins. J Am Chem Soc 125 8928-8935... 

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