Solving Protein Structures Using Restrained Molecular Dynamics and Simulated Annealing

10 Solving Protein Structures Using Restrained Molecular Dynamics and Simulated Annealing 

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 molecular dynamics is usually used in which additional terms, called penalty junctions, are added to the potential energy function. These extra terms have the effect of penalising conformations 

To obtain the electron density distribution it is necessary to guess, calculate or indirectly estimate the phases. Various methods have been developed to tackle the phase problem. For proteins the most common strategy is multiple isomorphous replacement in which the protein crystals are soaked in solutions containing salts of heavy metals such as mercury. 

Fig 9 22 Schematk illustration of an X-ra / scattering experiment The X-ray beam travels a different distance when scattered by an electron at the origin compared to an electron situated at r 

Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skiU which usually takes several years to acquire. 

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