In this study, we show that the SMP domain belongs to a superfamily of lipid/hydrophobic ligand-binding domains of known structure, which we call TULIP for tubular lipid-binding proteins, and propose a role for it in cellular phospholipid traffic.
In this work we identify A as the oxygen-binding position and propose a novel mechanism whereby the iron(IV oxo undergoes an isomerisation from R to R′ prior to hydrogen-atom abstraction.
In our previous paper, we explicitly derived the transient conditional probabilities for changes in binding site number and proposed a stochastic model for TFBS evolution (Wagner et al. 2007).
An adventitiously bound β-octylglucoside molecule, used in crystallization, enables us to model the binding of the true substrate and propose a metal-dependent mechanistic model for deacetylation.
Ham et al. [ 17] identified RNA-binding proteins involved in mRNA transport, and proposed a model in which a ribonucleoprotein complex moves in the phloem.
Together, the active peptide found and its suggested binding mode proposes a new strategy for inhibiting this enzyme and should aid the further design of novel, potent and non-peptidic G6PDH inhibitors.
We suggest that the conformational changes in Skp1 induced by glycosylation are responsible for enhanced binding to Fbs1 and propose that this represents a novel form of specific regulation of E3SCFUb ligases and contributes to the role of Skp1 glycosylation in O2 sensing in cells.
However, it has often been possible to propose common binding conformations and interactions through pharmacophore analysis, and this approach can be useful in understanding the requirements for binding and in proposing alternative scaffolds or substituents.
Within the C-terminus of the channel, a partially overlapping binding domain for calmodulin allows Ca2+-calmodulin binding and is proposed to destabilize the open state.
In particular, within GlpT, salt bridge interactions between helices H1, H7 and H8 are observed and predicted to re-arrange upon substrate binding, whereas in LacY Kaback and colleagues propose an interaction between helices H8 and H10, involving a salt bridge between Glu269 and His322, that facilitates substrate binding (He and Kaback, 1997).
