Brief Survey of Protein Motions

Some internal motions of proteins can be described quite simply. These include the localized vibrations within covalently bonded groups and also the elastic vibrations that involve coherent small-amplitude displacements of larger portions of the molecule. But generally, motions in proteins are more complex, 

Motions in proteins correspond to excursions on this energy landscape, and may be correspondingly complex. Even the simple motions mentioned at the outset of this section will be perturbed by transitions over barriers in the protein s energy landscape e.g., the localized vibrations of a covalently bonded group will differ to some extent, depending on which energy well in the landscape the biopolymer resides in. 

Recent single-molecule experimental studies of proteins provide more detailed views of protein motions, and confirm that a wide variety of timescales is involved in, e.g., catalytic action of enzymes [7,14,15,19,33], Of course, molecular dynamics simulations have been used to probe motions in single proteins for many years, and advances in both theory and computational science have made simulations a powerful approach to building theoretical understanding of protein dynamics [1], The recent introduction of accelerated molecular dynamics methods is helpful in this context [11]. Although detailed dynamical information is sacrificed to the enhanced sampling of conformational space in these methods, which have been shown to access conformational fluctuations that are revealed by nuclear magnetic resonance experiments on the millisecond 

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