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

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

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4). This is because interpretation of any pairwise binding measurement Assembly of transcription regulatory complexes quantitative analysis Purified components Protein assembly state Small ligand binding DNA binding Protein assembly Fig. 4 Outline for characterization of the pairwise interactions that may contribute to assembly of a transcriptional regulatory complex. Details of the methods that may be used to measure each pairwise interaction are provided in the text. 2. Linked Equilibria in Transcription Initiation 31 requires knowledge of the protein oligomeric state.

The approach just described requires the determination of a binding constant from duplex melting under saturating ligand conditions and its extrapolation from the melting temperature of the saturated complex to a far removed temperature of interest. 6  C temperature range. Such a large temperature extrapolation is unsatisfactory. A more rigorous estimate of the binding constant, as well as the binding site size, can be made with the application of McGhee’s statistical mechanical algorithm (McGhee, 1976) to the complete set of melting curves shown 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. Since the two pathways start and end at the same state, the following holds true: KLP KLP=D ¼ KPD KPD=L ð5Þ Furthermore, if linkage, either positive or negative, exists in the system, the following is also true: KLP 6¼ KPD=L ð6Þ 29 2.

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