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Background
Motions play an essential role in catalysis and protein-ligand interactions. Gerstein et
al.[3] classify these motions first on the basis of packing into shear, hinge (treated in this
work) , and “other,” then on the basis of size into fragment, domain, and subunit. A
subunit is a peptide fragment that is not covalently attached to a larger complex; subunit
motions are outside the scope of this work. Structural domains are defined in various
subtly different ways[111]; the definition of relevance to this work states that a domain is
stable unit of a protein, containing a hydrophobic core about which folding
nucleates[112]. Fragments are stretches of polypeptide too small to be considered
domains and are also outside of the focus of this work.
A representative set of motions from the Database of Macromolecular Motions was
classified on the above basis by Gerstein et al [3]. Hinge bending motions were found to
account for 45% of motions in a representative set comprising domain hinge motions
(31% of the total) and fragment hinge motions (14%)[3, 9, 25]. Thus understanding
fundamental aspects of hinge bending mechanisms may lead to an improved
understanding of the relationship between structure and function. As mentioned in this
work we focus on domain hinge motions.
There are three levels of hinge prediction. The easiest case occurs when the atomic
coordinates are available for two or more conformations of a given protein, e.g. the apo
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