Biomolecule conformational change

The several theoretical and/or simulation methods developed for modelling the solvation phenomena can be applied to the treatment of solvent effects on chemical reactivity. A variety of systems - ranging from small molecules to very large ones, such as biomolecules [236-238], biological membranes [239] and polymers [240] -and problems - mechanism of organic reactions [25, 79, 223, 241-247], chemical reactions in supercritical fluids [216, 248-250], ultrafast spectroscopy [251-255], electrochemical processes [256, 257], proton transfer [74, 75, 231], electron transfer [76, 77, 104, 258-261], charge transfer reactions and complexes [262-264], molecular and ionic spectra and excited states [24, 265-268], solvent-induced polarizability [221, 269], reaction dynamics [28, 78, 270-276], isomerization [110, 277-279], tautomeric equilibrium [280-282], conformational changes [283], dissociation reactions [199, 200, 227], stability [284] - have been treated by these techniques. Some of these... 

Thermal fluctuations are known to affect considerably the structure and other properties of biomolecules [30]. Recently, it was recognized that conformational changes in DNA can produce significant variations in the t-stacking of base pairs and thereby modulate the efficiency of charge transfer [31-33]. Thus, one has to employ a combination of molecular dynamics... 

When coupled with revolutionary advances in data analysis, whereby a low resolution three-dimensional electron density map may be recovered from the one-dimensional X-ray scattering profile, SAXS has now become a routine technique for characterizing conformational changes in biomolecules (Lipfert and Doniach, 2007 Petoukhov and Svergun, 2007 Putnam et al., 2007). To date such methods have been used to study proteins in solution. Only recently have these methods been applied to the study of RNA molecules in solution (Lipfert et al., 2007a). 

McCoy and Liapis [36] used two different kinetic models to represent the column affinity process. In both models the transport of the adsorbate in the adsorbent particle is considered to be governed by the diffusion into the pores. In model I the adsorption is assumed to be completely reversible with no interaction between the adsorbed molecules, In model 2, it is assumed that the biomolecule may change conformation after adsorption. Although these two models represent different overall adsorption mechanisms, the differences between the simulated breakthrough curves is very small. 

As is well-known, FRET is a powerful tool for sensing conformational changes in single biomolecules [92-94]. The first FRET study of a single dual-GFP construct was completed in the Moerner lab for the cameleon YC2.1 complex in 2000 [95]. Analysis of single-molecule signals from the... 

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