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Mutations in PAR affect DNA binding: changing Pro 87 or Pro 97 to Ala or Gly abrogates DNA binding and activity in vivo [17], while mutation of Arg 91 to Lys allows better in vitro binding and suppresses several loss-of-function mutations in the DBD [18], [19].
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If activator and repressor bind similarly to the same DNA binding sites, changing binding affinity would affect the probability of bound repressor or activator equally.
For example, the Z'-score between retinoic acid receptor gamma-2 (1EXX) and retinoic acid (REA) was -3.1, the lowest Z'-score of all drug-protein bindings, was always classified as the true binding while changing the classifying threshold.
We tested whether presence of an SGK phosphorylation site between the domains might influence binding, however changing Ser327 to either Ala or Asp did not alter binding to SGK (Fig. 1D).
Via modification of these gels with RGD (Arg-Gly-Asp) sequences for integrin binding and changing the concentration of peptide, KFE gels can be fabricated to allow tuning of cell binding, matrix compliance, and pore size.
Our findings of an alternative allostery of P-selectin Lec domain also supported the prediction that the presence of EGF domain regulated the P-selectin-PSGL-1 binding by changing the conformation of Lec domain upon EGF orientation [7], where the S1' conformation favored the extended EGF orientation than that of S1 conformation (Fig. 8).
The inverse agonist N-methylscopolamine slowed GDP dissociation and GTPγS binding without changing affinity for GDP.
We demonstrate that the microdeletions mostly affect IC1 function and CTCF binding by changing CTS spacing.
This loop has been suggested to affect nucleotide binding by changing the conformation of a following loop [ 36].
This non-invasive method for switching cell activity can target specific cells through protein binding by changing the QD surface chemistry.
We only trained a predictor if the closest PDZ domain has ≥ 10 binding peptides (changing this threshold to nearby values does not affect our conclusions).
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