Molecular_motion-dynamics - Molecular motion and protein...

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Molecular motion and protein folding Protein Motion - Molecular Dynamics 1. Thermal motion Proteins are not static and rigid structures. The polypeptide backbone and specially the side chains are constantly moving due to thermal motion or kinetic energy of the atoms (Brownian motion). Thermal motion - displacement of functional groups - is necessary for protein catalysis (high substrate specificity & transition state stabilization) and allostery (transmit information to other units in a protein complex). When studying the structure of a protein, different techniques give different information about motion in macromolecules. X-ray crystallography allows a time averaged 'snapshot' of the structure, which appears as if it were frozen. Electron microscopy too gives fixed structures due to the long exposure time. NMR enables a time resolved, dynamic structure. Specially small domains and loops may fluctuate rapidly and are not resolved by crystallography, but may be accessible for NMR. Indirect evidence for flexible parts in 'frozen' structures comes from incomplete or unresolved parts of the protein. However, it does not give any information about the nature of this flexibility. From the point of view of a dynamic system, the native structure of a protein is a collection of conformational substates that have statistically equal stabilities . Experimental evidence for the importance of molecular motion in catalysis has been obtained using a small, globular protein, Ribonuclease A . At temperatures below 212 ° K where the fold is basically frozen but solute diffusion is still fast, substrate does not bind nor does bound substrate dissociate (even within
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Molecular_motion-dynamics - Molecular motion and protein...

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