Biological molecule conformations

Molecular Orbital Studies of Biological Molecule Conformations... 

A particularly important application of molecular dynamics, often in conjunction with the simulated annealing method, is in the refinement of X-ray and NMR data to determine the three-dimensional structures of large biological molecules such as proteins. The aim of such refinement is to determine the conformation (or conformations) that best explain the experimental data. A modified form of molecular dynamics called restrained moleculai dynarrdcs is usually used in which additional terms, called penalty functions, are added tc the potential energy function. These extra terms have the effect of penalising conformations... 

Nonnal mode analysis was first applied to proteins in the early 1980s [1-3]. Much of the literature on normal mode analysis of biological molecules concerns the prediction of functionally relevant motions. In these studies it is always assumed that the soft normal modes, i.e., those with the lowest frequencies and largest fluctuations, are the ones that are functionally relevant. The ultimate justification for this assumption must come from comparisons to experimental data. Several studies have been made in which the predictions of a normal mode analysis have been compared to functional transitions derived from two X-ray conformers [4-7]. These smdies do indeed suggest that the low frequency normal modes are functionally relevant, but in no case has it been found that the lowest frequency normal mode corresponds exactly to a functional mode. Indeed, one would not expect this to be the case. 

Circular dichroism (c.d.) spectroscopy measures the difference in absorption between left- and right-circularly polarized light by an asymmetric molecule. The spectrum results from the interaction between neighboring groups, and is thus extremely sensitive to the conformation of a molecule. Because the method may be applied to molecules in solution, it has become popular for monitoring the structure of biological molecules as a function of solvent conditions. 

Hansmann, U. H. E., Parallel tempering algorithm for conformational studies of biological molecules, Chem. Phys. Lett. 1997, 281, 140-150... 

As we have seen above, FRET is a technique that provides precise information about distances between 10 and 100 A which is in the range of the size of biological molecules and proteins. Researchers have taken advantage of this feature and developed different strategies to synthesize FRET sensors that are able to follow in real time and with high sensitivity very diverse processes such as enzymatic activity, conformational change, or molecule-molecule interaction. The design of these FRET sensors is described below. 

J. M. Wang, P. Cieplak, and P. A. Kollmann, How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules J. Comput. Chem. 21, 1049 1074 (2000). 

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