Protein conformation space

Heuberger and co-workers obtained, by using eSFA, a very intriguing result. Their data indicate that there exists a fine structure embedded within the established steric repulsion of PEG in the brush regime (Fig. 15) [159] arising due to restriction of the conformational space of the PEG/water complex, which causes quantisation of the steric force observed in the SFA. The presence of this water-induced restricted conformation space was suggested to have implications in protein adsorption since in order to adsorb a protein induces a local deformation, which necessitates a restriction of the PEG and protein conformational space, which is energetically and kinetically unfavourable [159, 160]. 

Recently, much progress has been achieved in various methods of discretization [156,157] of protein conformational space [42] and in the analysis of the fidelity of such discretizations [14,156,158-160]. 

A newer (2006) account on methods, problems, and goals of biomolecular simulations is given in a comprehensive article by Van Gunsteren (2006). Focused mainly on proteins, a very informative paper by Adcock and McCammon provides an excellent description of methods and key results from MD maybe found. (Adcock and McCammon 2006). New methodological advances were also reviewed at the same time Chu et al. popularize multiscale simulations (Chu et al. 2007), while Fiber et al. comment on the current literature on long time simulation methods (Dal Peraro et al. 2005) and Liwo et al. on efficient methods of sampling of proteins conformational space (Liwo et al. 2008). 

Affentranger, R., Tavernelli, I., Di lorio, E. E. (2006). A novel Hamiltonian replica exchange MD protocol to enhance protein conformational space sampling. Journal of Chemical Theory and Computation, 2, 217. 

Simulations of the dynamic motion of proteins aim at sampling relevant portions of the conformational space accessible to the proteins under the influence of environmental variables such as temperature, pressure, and pH. We... 

All of the conformational search methods that were described in Sections 9.2-9.7 have bee used at some stage to explore the conformational space of small pephdes. Here we wi describe some of the methods designed specifically for tackling the problem for peptide and proteins. 

Equations (5)-(8) assume that the energy functions (7 and Ub operate on the same conformation space i.e., A and B must have the same number N of degrees of freedom. In practice, this almost always implies that A and B have the same number of atoms or particles. Most biochemical changes of interest (e.g., point mutations of a protein) do not obey this requirement, but they can often be made to do so artificially through the use of dummy atoms (see below). 

DA Elmds, M Levitt. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 243 668-682, 1994. 

If the expanded denatured state is trapped in small region of conformation space where all chains have the correct topology, how did it get there To this question there is but one answer. A fraction of the free energy of ATP hydrolysis consumed during protein translation is used to... 

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