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4.0 Identification of Secondary Structure

Thus far we have seen classical examples of helices, sheets and turns and I think most would agree that there would be little difficulty in identifying these secondary structures if the figures were left unidentified. However, locating secondary structures in three-dimensional structures of proteins is a different matter. Sure helices are different from sheets and (most) turns, but a computer algorithm will need an exact definition. As you might guess, quite a few definitions exist, each reflecting the authors biases and agendas. Of course, none of these definitions are wrong and unfortunately, none are suited to all purposes. Some common criteria for identifying secondary structures are outlined in the following section.

Despite the best efforts of crystallographers and NMR spectroscopists, the three-dimensional structures of the vast majority of proteins for which primary sequence information is available are lacking. Fortunately, many interesting questions can be explored and answered without knowledge of the exact three-dimensional structure. A number of experimental techniques can selectively examine certain general aspects of macromolecular structure while completely ignoring others - usually with relatively little investment of time and sample. Reasonable estimates of protein secondary structure content can be determined empirically (with varying success) through the use of "Circular dichroism spectroscopy" , "NMR spectroscopy" , or "FT-infrared spectroscopy" techniques. Section 4.3 will cover yet another possibility - prediction of secondary structure.

4.1 - Identification in 3D Structures
Angle plots
Hydrogen bonds
Distance plots
4.2 - Identification without 3D Structure
4.2.1 - Circular dichroism spectroscopy
4.2.2 - NMR spectroscopy
4.2.3 - FT-infrared spectroscopy
4.3 - Prediction of Secondary Structure
4.3.1 - homology
4.3.2 - statistical
4.3.3 - stereochemical

No Title - 31 MAY 96
written by Kurt D. Berndt, Karolinska Institute, Stockholm, Sweden
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