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One of the two binding sites may interact with carbohydrates on the neutrophil surface, and the other site binds to glycoconjugates in the extracellular matrix.
We recognize there are several limitations in our methodology: only several forms of cooperative functions were tested while the actual function may be much more complex; and in the thermodynamic model, only immediately adjacent binding sites may interact with each other, an assumption taken for the ease of computation without much theoretical justification.
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The inhibition model of a mixed-type inhibitor is defined as unequal binding of the inhibitor to E and ES and suggests that AP5 that contains a portion of the factor Xa binding site may also interact with prothrombin in association with prothrombinase (53).
Accordingly, promoters that have the appropriate factor binding sites may be restricted, via chromatin organization, from interacting with a transcription factor under specific cellular conditions.
Therefore, true binding sites may have SNPs less frequently than the non-binding sites.
A lost binding site may have been replaced with a new, species-specific binding site - i.e. binding site turnover.
However, the acquisition of quantitative information is no small task, in part because signaling proteins contain multiple phosphorylation sites and may interact with multiple binding partners.
To identify the binding factors that may interact with CR4.2, we first used MatInspector in Genomatix Suite (München, Germany) (Quandt et al., 1995; Werner, 2000; Cartharius et al., 2005) to search for potential trans-acting factor binding sites on CR4.2.
Antagonists mediate their effects by binding to the active (orthosteric = right place) site or to allosteric (= other place) sites on receptors, or they may interact at unique binding sites not normally involved in the biological regulation of the receptor's activity.
Under this picture: binding sites of TFexp directly attract TFexp, and sites of other factors may interact cooperatively with TFexp, thus indirectly recruiting TFexp.
In addition, antagonists may interact at unique binding sites not normally involved in the biological regulation of the receptor's activity to exert their effects.
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