Restrained X-ray refinement

Methods for simulating restrained x>ray refinement data from molecular dynamics trajectories. 

The additional penalty function that is added to the empirical potential energy function in restrained dynamics X-ray refinement has the form ... 

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... 

Thioredoxin from E. coli has been studied extensively using biochemical, spectroscopic and X-ray diffraction techniques. The protein consists of a single polypeptide chain of 108 amino acid residues of known sequence. The protein has been cloned and expressed. Thioredoxin of E. coli is a compact molecule with 90% of its residues in hehces, beta-strands or reverse turns. This protein transports electrons via an oxidation-reduction active disulfide". The oxidized form thioredoxin-(S2) is reduced to thioredoxin-(SH)2. In particular, this protein was found to participate in the reduction of ribonucleotides to deoxyribonucleotides. In Fig. 1, the optimized stracture is shown with a carbon backbone for clarity only. The molecule consists of two conformational domains, connected by two helices. The beta-sheet forms the core of the molecule packed on either side by clusters of hydrophobic residues. Helices form the external surface. We used a crystal stracture of the oxidized form of thioredoxin from Escherichia coli that has been refined by the stereochemically restrained least-squares procedure at 1.68 A resolution". ... 

Recently, Lindorff-Larsen el al.uo included the order parameter (S 2) in the target function, and refined an ubiquitin X-ray structure by restrained molecular dynamics (Section 6.4) to obtain an NMR structure ensemble (Section 6.5) from the trajectories. They simulated the values of RDCs (Section 9.1) and side chain scalar coupling from the calculated ensemble to confirm that the method can determine the protein three-dimensional structure and dynamic structure simultaneously. The simulated values were in good agreement with the corresponding measurement data. The simulation accuracy was improved from the preliminary calculated structure without the order parameters. The approach is typically important, because they tried to link the ensemble with a dynamic structure directly. 

Jack and Levitt introduced molecular modelling techniques into the refinement in the form of an energy minimisation step (using a force field function) that was performed alternately with the least-squares refinement [Jack and Levitt 1978]. This approach was shown to give convergence to better structures. More recently, restrained molecular dynamics methods were introduced by Brunger, Kuriyan and Karplus [Brunger et al. 1987]. These methods have had a dramatic impact on the refinement of X-ray and NMR structure of proteins. 

Recently, the structure of l,2,3,4,5,6,7,8-octahydro-l,2,4,5-tetrazino[l,2- ][l,2,4,5]tetrazine 101, prepared from paraformaldehyde 100 and hydrazine hydrate, was solved by simulated annelating from X-ray laboratory powder data and refined by Rietveld refinement without any restrains for non-H-atoms (Scheme 25) <2006AXEol449>. 

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