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In this form, the active site groove is exposed, providing an alternative model for ligand binding studies.
In each case, the structures should be interpreted in the context of a kinetic thermodynamic model for ligand binding and catalysis.
The reviewers and I also think that a few additional (and incisive) tests of the model for ligand recognition, using site-directed mutagenesis and functional testing, would greatly strengthen the paper.
We recently presented a model for ligand binding, higher-order receptor oligomerization, and receptor phosphorylation that reproduced our biophysical and biochemical experiments with EGFR eGFP in BaF/3 cells.
Adapting the McGhee and von Hippel model for ligand binding to a linear lattice [33], we analyzed the effect of actin truncation on TM affinity to an isolated binding site and an equilibrium constant for moving TM from an isolated binding site to a singly contiguous binding site, which is a measure of binding cooperativity [11,31,34].
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The most widely used model for ligand-dependent receptor activation is described by the so-called extended ternary complex, and its extension, the cubic ternary complex.
To better understand this extraction process, we develop a model for ligand-exchange chiral extraction which couples a complete description of chemical equilibria in each phase with the overall phase equilibria of the system.
The model for ligands was not included until their conformations were fully defined by unbiased | Fo| – | Fc| ϕcalc electron density maps.
The model for ligands was not included until their conformations were fully defined by unbiased | Fo| – | Fc|, φcalc electron density maps.
A first class of approaches, called ligand-based chemogenomics by Rognan (2007), pool together targets at the level of families (such as GPCR) or subfamilies (such as purinergic GPCR) and learn a model for ligands at the level of the family (Balakin et al., 2002; Klabunde, 2006).
This table defines a standard space of K hypothesis g models for ligand induced protein dimerization equilibria.
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