Analysis of ligand binding mechanism by dimeric receptors using stopped-flow fluorimetry—application to the human decapping scavenger enzyme

Abstract

Association of a ligand with the binding site of a receptor is usually at least a two-step process - formation of an initial encounter complex followed by a conformational transition of the complex. Consequently, the description of binding by dimeric receptors requires a two-dimensional reaction scheme. An interesting example of a dimeric receptor is the decapping scavenger enzyme, DcpS. It is a critical determinant of mRNA metabolism that hydrolyses the 5’-end \(\hbox {m}^7\)GpppN cap following 3’-end mRNA decay. The DcpS family of proteins function as homodimers with one active site in each protomer. We investigate the binding of substrate and product analogues of the mRNA cap, \(\hbox {m}^7\)Gp(\(\hbox {CH}_2\))ppG and \(\hbox {m}^7\)GMP, respectively, by human DcpS wild-type (\(\hbox {DcpS}^{\mathrm {WT/WT}}\)) and its one-site compromised mutant (\(\hbox {DcpS}^{\mathrm {WT/BC}}\)) using stopped-flow fluorimetry. Based on observations for the mutant \(\hbox {DcpS}^{\mathrm {WT/BC}}\), binding by each active site and for each ligand proceeds through the formation of an encounter complex followed by conformational transitions. In the case of \(\hbox {DcpS}^{\mathrm {WT/WT}}\), we show that only two association rate constants, one for the apo-enzyme with both sites empty and the second for the enzyme with one site already occupied, can be determined with satisfactory accuracy from experimental progress curves, even for experimental data with a high signal-to-noise ratio. An interesting and biologically relevant observation is that binding of substrate analogue by one site prevents binding by the remaining empty site, whereas in the case of the \(\hbox {m}^7\)GMP product both sites bind ligand independently of the binding state of the other site.