Direct Measurement of Through‐Bond Effects in Molecular Multivalent Interactions

Abstract

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Advances in the Biological Application of Force-Induced Remnant Magnetization Spectroscopy

“…The fluid shear could have merit over SURFS in controlling the force more precisely. Feng and co-workers used a parallel-plate flow chamber to apply fluid shear force and analyzed the through-bond effects on the bivalent binding of the thrombin–aptamer complex ( Figure 4 d) [ 39 ]. The satisfactory results were expected to design high-performance ligands efficiently.…”

Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands

“…Experimental reports of the thrombin exosite long-range communications emerged from the analysis of the binding affinities of ligands belonging to different chemical species and from the variation of the biophysical properties of one exosite after a ligand binding at the other. Indeed, evidence of the occurrence of long-range mutual effects between the two exosites has been obtained by using a repertoire of different biophysical techniques (fluorescence, hydrogen-deuterium exchange/NMR, SPR, backscattering interferometry, and FIRMS) [ 106 , 107 , 108 , 110 , 148 , 149 , 150 , 151 , 152 , 153 , 154 ]. A qualitative summary of the outcome of these experiments is reported in Table S9 .…”

“…Notably, the effect of the TBA is dependent on the ligand at the exosite II. Indeed, the binding of the TBA aptamer at the exosite I increases the affinity of the HD22 aptamers at the exosite II [ 108 , 110 ]. As for the hirudin/sF2 pair of ligands [ 149 ], the mutual interplay between the exosites operates in both directions also for the TBA/HD22 ligands [ 108 , 110 ].…”

“…Indeed, the binding of the TBA aptamer at the exosite I increases the affinity of the HD22 aptamers at the exosite II [ 108 , 110 ]. As for the hirudin/sF2 pair of ligands [ 149 ], the mutual interplay between the exosites operates in both directions also for the TBA/HD22 ligands [ 108 , 110 ]. For other exosite II ligands, the effects produced on the affinity at the exosite I are varied.…”

“…This is somewhat surprising considering the remarkable results recently achieved in the definition of the long-distance and dynamic allosteric regulation of this protein [ 106 , 107 ], a topic in which the experimental and computational characterizations of thrombin complexes with aptamers, either single-stranded DNA or RNA molecules, which selectively bind to a specific target, have played a major role [ 108 , 109 , 110 , 111 , 112 ]. To fill this gap and to attain an up-to-date view of thrombin structural biology, we couple a survey of literature papers with an extensive analysis of PDB content.…”