By Wolfram Saenger, Udo Heinemann
Protein-nucleic acid interactions were a focus of medical curiosity and learn during the last 3 a long time. This quantity features a sequence of essays which describe quite a number difficulties within the box, investigated via a number of thoughts. An introductory bankruptcy on DNA-protein interactions within the law of gene expression is via papers on chosen version structures. those disguise numerous orders of importance in dimension, going from small proteins via Lac repressor headpiece and RNase T1 to chromatin. the purpose of the textual content has been to mirror the range of difficulties even during this well-defined clinical box, and to supply researchers with the entire vital recommendations presently used to check the interactions.
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Additional resources for Protein-Nucleic Acid Interaction
Calculate family of structures using geometric constraints only (experimental constraints plus covalent structure), using, for instance, distance geometry (DG) and distance bounds driven dynamics (DDD). Refine these structures usir:g geometric constraints and potential energy functions, for instance, with restrained energy minimization (REM) and restrained molecular dynamics (RMD). , 1979, 1983; Havel and Wuthrich, 1985) calculates structures from geometric constraints in the form of upper and lower bounds on atom-atom distances.
The exact distribution of the dichroism amplitudes might be influenced by a potential contribution of the protein dipole to the orientation mechanism, which is dominated by the large DNA polarizability. Model calculations with several orientations of a protein dipole showed that the slow process prevails in all cases of practical interest. Another complication may result from the relative position of the two protein dimers around the DNA, which is not exactly known. However, alignment of the proteins at opposite sides of the DNA, rather than at the same side, leads to an increase of the rotation time constant by not more than about 5 ns.
4, the DNA has to be wrapped around the protein to a very close contact and at a radius of curvature 44 A, in order to come reasonably close to the experimental time constant of 130 ns. In this case, bending of the DNA approaches the maximal value compatible with the protein structure. Simulation of the experimental data observed for other DNA fragments and/or for other conditions did not reveal the same extreme degree of bending, but considerable bending of the DNA has been deduced for most specific complexes.
Protein-Nucleic Acid Interaction by Wolfram Saenger, Udo Heinemann