Conformational Dynamics and Molecular Recognition: Backbone Dynamics of the Estrogen Receptor DNA-binding Domain

Effects of Phosphorylation on the Structure and Backbone Dynamics of the Intrinsically Disordered Connexin43 C-terminal Domain

“…7B) also indicate fast nanosecond to picosecond time scale dynamics consistent with the TM4-Cx43CT being an IDP. R 1 and R 2 values of structured protein are ϳ2 and 4 times greater than the corresponding values of a disordered protein of similar size, respectively (56,57). 1 H-15 N NOE data are also consistent with fast dynamics (Fig.…”

Indirect DNA Readout on the Protein Side: Coupling between Histidine Protonation, Global Structural Cooperativity, Dynamics, and DNA Binding of the Human Papillomavirus Type 16 E2C Domain

“…This result confirms for HPV16 E2C the "protein-dependent indirect readout" that was previously deduced from structural considerations and thermodynamic measurements on homologous E2C-DNA complexes 16,17,33,35,38 and observed in other systems. [7][8][9][10][11][12][13] Interestingly, the different conservation levels of the five E2C histidines in human genital papillomaviruses (Bose et al 53 and Fig. S5) correlate with the degree of coupling between DNA binding and side-chain protonation.…”

“…1 Histidine side chains often take part in direct readout, 2-6 providing a plausible regulatory mechanism under physiological conditions due to their intrinsic pK a of 6.3. Second, the dynamics of the globular domain [7][8][9][10][11][12][13] and, in particular, the target DNA sequence 1,14-18 modulate binding through indirect effects. This "indirect readout" can couple DNA binding to protein dimerization and other molecular functions through allosterism.…”

“…This "indirect readout" can couple DNA binding to protein dimerization and other molecular functions through allosterism. 7,8,12,19,20 Human papillomaviruses (HPVs) are highly prevalent pathogens of epithelial tropism. 21,22 Mucosal HPV types are the etiological agents of cervical cancer, the second most common cancer in women, and of vaginal, anal, penile, and head and neck cancers.…”

Modeling zinc sulfhydryl bonds in zinc fingers

“…Figure 6 shows the generalized order parameters S 2 calculated from the 1glu and 2gda simulations. The corresponding experimental NMR values [6,20] are drawn as solid gray squares, and for those residues not determined, crossed squares are depicted. Again good agreement between simulation and experimental data is seen in the order of S …”