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Biological background of adenylate kinases


    X-ray diffraction analyses yield accurate static structures of crystalline proteins. With the advent of recombinant proteins, the number of elucidated protein structures increased greatly. Among them are more and more homologous structures that can be related to each other. Very often, homologous structures have different ligands and/or occur in different crystal packings, giving rise to conformational variations. A family with particularly large conformational changes are the NMP kinases (belonging to the adenylate kinase family as named after the first established structure) that catalyze the reaction:


                                N1TP Mg(2+) + N2MP ⇔ N1DP + Mg(2+) + N2DP


where N1 and N2 stand for nucleotide bases. Here, we relate these structures to each other, work out the changes, sort the static pictures along trajectories and combine them into a movie. The presented movie shows the motions during a catalytic cycle, which lasts about 1 to 3 milliseconds in this enzyme family.      

    For a long time, it has been suggested that kinases undergo considerable movements during catalysis, because they have to shield their active center from water in order to avoid ATP-hydrolysis. Trying to verify the expected conformational changes, the small NMP kinases have been studied extensively. The large number of elucidated NMP kinase structures confirmed the expectations. T

hese structures allowed to follow the motions closely, because various intermediate states are frozen in crystals. We found that the frozen position of a domain depends on the ligand and on crystal packing forces giving rise to numerous states. An ordering of these states using computational smoothing makes a movie representation possible. Such a movie depicts the action of a protein much more accurately than a single structure can; it represents a novel vehicle for passing on our knowledge of life at the atomic level. The established NMP-kinase structures are listed in the publication: Clemens Vonrhein, G. J. Schlauderer and Georg E. Schulz (1995). Structure 3, 483-490.

The NMP-kinase movie of 1995 was the first of its kind. Since isolated static structures indicating large motions are also known for other proteins, many more of such movies have been produced in the following.




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