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Biology LibreTexts

7: Protein Structure

eading & Problems:LNC 115-124, 125-143

Protein sequencing by mass spectrometry (MS)

Mass spectrometry is a method that can separate molecule by charge/mass ratio and can determine their masses to up to six to eight decimal places. As a result, the exact composition of peptides can be determined. The method can be used to recursively break the peptide and evaluate the product to determine the sequence. It can also be used to determine what proteins are in complex protein mixtures, and their relative quantities (e. g. as in all the proteins in a sample of tissue). These methods are widely used today. You can read more on this in LNC pages 100-102, but the book provides more detail than I expect you to know.

I. Structure of the peptide bond. (Image Source:

II. Secondary structure - backbone-backbone interactions form repeated structures.

B. external link: ß-sheet, two kinds parallel and antiparallel. !!This site requires Java and may be blocked in your browser!!


Anti-Parallel                                                                                    Parallel

C. ß-turn (hairpin turn)

III. Tertiary structure.

A. Example: Dr. Gasser's JSmol version of external link: Myoglobin or this Jmol view, external link: Myoglobin2.

C. Example: Cyclophilin. To view this go to the following link and click the "Submit Request" button (if there is a problem, be sure that "jMol PDB Viewer" is selected in the upper right menu). Here is the external link: Cyclophilin link. !!This site requires Java and may be blocked in your browser!!

D. You can search among all known protein structures at the NIH "external link: Molecules To Go" site and view them as described above.