Words similar to conformational
Example sentences for: conformational
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This bias normally influences both the orientation and conformation of the ligand in the active site, which usually represents a local minimum conformation [ 14 ] . More importantly, the lock and key concepts used to evaluate enzyme-substrate binding, in reality, refer to flexible locks and keys that are both in constant dynamic (thermal) motion [ 15 ] . For example, an analysis of conformational changes upon complex formation for a representative set of 39 pairs of ligand-free and ligand-bound structures showed that 50% of these proteins undergo substantial main-chain and side chain conformational changes when the ligand is bound [ 15 ] .
For example, Herschlag and co-workers have previously shown that a nucleobase could complement an abasic site within the hammerhead ribozyme, restoring cleavage activity [ 1 ] . Similarly, Porta and Lizardi engineered a hammerhead ribozyme that assumed an inactive secondary structure; upon the addition of an oligonucleotide that disrupted the engineered secondary structure, the ribozyme was activated [ 2 ] . More recently, it has previously been shown that many selected nucleic acid binding species (aptamers) undergo conformational changes upon ligand binding [ 3 4 5 6 ] In addition, when aptamers are conjoined to ribozymes, the ligand-induced conformational changes in the aptamers frequently modulate the structures and hence the activities of the ribozymes [ 7 8 9 ] For example, binding of theophylline to the anti-theophylline aptamer [ 10 ] modulates the conformation of residue [ 11 12 ] and the overall stability of the aptamer [ 10 13 ] . Appending the anti-theophylline aptamer to the hammerhead ribozyme allowed cleavage activity to be modulated by 110-fold by theophylline [ 13 ] . Similarly, appending the anti-theophylline aptamer to a small ribozyme ligase (L1) generated an aptazyme that was activated 1,600-fold by saturating theophylline concentrations [ 14 ] .
This interaction unclasps the complex between the cytoplasmic tails, which then allows a conformational shift in the extracellular domain from a bent to a more extended form for high-affinity ligand binding (Figure 1) (Takagi et al.
Future work will be devoted to examining a range of functionalized organic molecules in order to define the boundary of molecular polarity within which standard conformational search methodology can be applied with confidence.
To gain further details for this model of enzyme action, we are characterizing the protein-protein interactions between the Top67 transesterification domain and the ZD domain, as well as the protein conformational changes that can take place when the enzyme interacts with DNA substrate.
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