Download e-book for kindle: Protein-Nucleic Acid Interactions: Structural Biology (RSC by Phoebe A. Rice, Carl C. Correll

By Phoebe A. Rice, Carl C. Correll

ISBN-10: 0854042725

ISBN-13: 9780854042722

This booklet presents either in-depth heritage and updated details during this zone. The chapters are prepared via normal subject matters and rules, written by means of specialists who illustrate subject matters with present findings. themes coated contain: - the function of ions and hydration in protein-nucleic acid interactions- transcription elements and combinatorial specificity- oblique readout of DNA series- single-stranded nucleic acid binding proteins- nucleic acid junctions and proteins, - RNA protein reputation- attractiveness of DNA harm. it will likely be a key reference for either complicated scholars and verified scientists wishing to increase their horizons.

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57 As an alternative to these computational/empirical methods, it would be highly desirable to have a direct experimental determination of water release during macromolecular association. One approach is based on the idea that the perturbation of association equilibrium by small-molecule osmolytes (or ‘‘cosolutes’’) can be used to measure the stoichiometric release of water qlnKA/qlnaw –433 (À383)c –350 qlnKA/qlnaw –2188, –2508 À80 –80 À470 (À414)c À430 DNw EcoRV 165 À88 –100 DG1HE (kcal mol –1) qlnKA/qlnaw –2006, –2050 DASA (A˚2) Nonpolar, polar –407 (À357)c –356 DNw BamHI À80 –88 DG1HE (kcal mol –1) Solvent accessible surface areas (ASA) were calculated using the program NACCESS (version July, 1996), which had been modified to include van der Waals radii and atom types for DNA.

115,120–123 If the data points are few, and/or if an insensitive assay for protein-DNA binding restricts measurements to the low-salt range, imposing a linear fit on the data across this region of changing slope will underestimate the salt dependence significantly. , a shift from dimers to tetramers) leading in the 30 Chapter 2 125 limit to protein precipitation. Few published studies take account of this possibility. In our experience with EcoRI, BamHI and EcoRV endonucleases (M. Kurpiewski and L.

4 kcal molÀ1 KÀ1. 5 kcal molÀ1 KÀ1 for these systems27, the interfacial water contribution is significant but not dominant. In addition to this, the release of water from protein and DNA surfaces probably 28 Chapter 2 makes a smaller contribution to the negative DC1P, so that all hydration terms together account for less than half the observed DC1P. By contrast, in studies of the interaction of an archaeal TBP with DNA,36 large changes in DC1P were observed upon mutational perturbation of a network of five to seven water molecules lying in a highly charged cleft.

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Protein-Nucleic Acid Interactions: Structural Biology (RSC Biomolecular Sciences) by Phoebe A. Rice, Carl C. Correll

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