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Approximate values for force constant and wave number associated with a low-frequency concerted motion in proteins can be evaluated by a comparison of X-ray structures.

Merlino A, Sica F, Mazzarella L

Dipartimento di Chimica, Università degli Studi di Napoli Federico I", Via Cynthia, 80126 Napoli, Italy.

Low-frequency internal motions in protein molecules play a key role in biological functions. A direct relationship between low-frequency motions and enzymatic activity has been suggested for bovine pancreatic ribonuclease (RNase A). The flexibility-function relationship in this enzyme has been attributed to a subtle and concerted breathing motion of the beta-sheet regions occurring upon substrate binding and release. Here, we calculate an approximate value for the force constant and the wave number of the low-frequency beta-sheet breathing motion of RNase A, by using the Boltzmann hypothesis on a set of data derived from a simple conventional structural superimposition of an unusual large number of X-ray structures available for the protein. The results agree with previous observations and with theoretical predictions on the basis of normal-mode analysis. To the best of our knowledge, this is the first example in which the wave number and the force constant of a low-frequency concerted motion in a protein are directly derived from X-ray structures.

Published 10 May 2007 in J Phys Chem B, 111(19): 5483-6.
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