Techniques

Biophysical Tools for Biologists, Volume One: In Vitro by Dr. John J. Correia and Dr. H. William Detrich, III (Eds.)

By Dr. John J. Correia and Dr. H. William Detrich, III (Eds.)

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Extra resources for Biophysical Tools for Biologists, Volume One: In Vitro Techniques

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Depending on the protein, small molecule binding can result in relief of transcription repression by decreasing occupancy at an operator sequence or can enhance repression or activation by increasing occupancy. In eukaryotic systems, the nuclear receptors provide examples of Linked equilibria in assembly of transcription regulatory complexes Small ligand binding and protein assembly Small ligand binding and DNA binding Protein association and DNA binding Fig. 2 Coupling of the individual pairwise interactions in assembly of a transcriptional regulatory complex.

University Science Books, Mill Valley, CA. , and Zhang, Z. Y. (1998). Low-aYnity binding determined by titration calorimetry using a high-aYnity coupling ligand: A thermodynamic study of ligand binding to protein tyrosine phosphatase 1B. Anal. Biochem. 261, 139–148. Suggested Reading Connors, K. A. (1987). ’’ John Wiley & Sons, New York. A useful survey of methods for the determination of binding isotherms and the interpretation of binding data. Written from a pharmacological perspective. Edsall, J.

Proteins to which small ligands can bind to alter DNA binding and, ultimately, transcription initiation. An illustration of linkage between small ligand and DNA binding is shown in the thermodynamic cycle in Fig. 3. The two binding processes can occur by two alternative pathways, ligand followed by DNA binding or DNA followed by ligand binding. The equilibrium expressions corresponding to these two pathways are shown in the following equations: KLP ¼ ½LŠ½PŠ ½LPŠ ð1Þ KPD ¼ ½PŠ½DŠ ½PDŠ ð2Þ KLP=D ¼ ½LPŠ½DŠ ½LPDŠ ð3Þ KPD=L ¼ ½PDŠ½LŠ ½LPDŠ ð4Þ In this case, the expressions are presented in terms of dissociation and the constants, K, are therefore equilibrium dissociation constants.

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