Lac repressor headpiece

Boelens, R., et al. Complex of lac repressor headpiece with a 14 base-pair lac operator fragment studied by two-dimensional nuclear magnetic resonance. /. Mol. Biol. 193 213-216, 1987. 

A review is given of the application of Molecular Dynamics (MD) computer simulation to complex molecular systems. Three topics are treated in particular the computation of free energy from simulations, applied to the prediction of the binding constant of an inhibitor to the enzyme dihydrofolate reductase the use of MD simulations in structural refinements based on two-dimensional high-resolution nuclear magnetic resonance data, applied to the lac repressor headpiece the simulation of a hydrated lipid bilayer in atomic detail. The latter shows a rather diffuse structure of the hydrophilic head group layer with considerable local compensation of charge density. 

F. Culard, M. Schnarr, and J. C. Maurizot, Interaction between the lac operator and the lac repressor headpiece Fluorescence and circular dichroism studies, EMBO J. 1, 1405-1409 (1982). 

Figure 14.14. The 500-MHz 1H 2D NOESY spectrum of the lac repressor headpiece in H2O. (From ref. 4. Copyright 1985 by John Wiley Sons, Inc. Reprinted by permission.)...

This method of refinement was first applied, using the distance restraint form of Eq. [9], to the lac repressor headpiece using a model as the initial structure.9-83 It was later applied to a heptadecapeptide.84 Subsequent studies with model data showed that, with a carefully chosen simulation protocol, the method was capable of refining even poor starting structures.85 86... 

Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data A lac Repressor Headpiece Structure Based on Information on /-Coupling and from Presence and Absence of NOEs. 

Based Molecular Dynamics Simulation of the Interaction of the lac Repressor Headpiece and Its Operator in Aqueous Solution. 

J. De Vlieg, R. Boelens, R. M. Scheek, R. Kaptein, and W. F. van Gunsteren, hr. J. Chem., 27, 181 (1986). Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data A lac Repressor Headpiece Structure Based on Information on J-Coupling and from Presence and Absence of NOE s. 

Remarks sequence is symmetric lac operator site present residue numbering differs from the one used in reference. Additional data in ref NH proton spectrum of the DNA in the free state and saturated with lac repressor headpiece... 

The lac repressor headpiece in complex with its operator (Figure Id) was simulated using distance restraints from NMR studies, with a 50 ps piece of unrestrained trajectory. From this simulation the specific contacts between the protein and the DNA were found to be formed mainly by non-polar contacts, and to a lesser extent through water mediated hydrogen bonds. 

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