Analysis of the binding of ligands to large numbers of sites: the binding of tryptophan to the 11 sites of the trp RNA-binding attenuation protein.
Analysis of the cooperative binding of ligands may provide insight into the underlying mechanisms of biological control. Binding of L-tryptophan at each juncture in the ring of 11 subunits of the trp RNA-binding attenuation protein exhibits cooperativity. To analyze binding of this kind we have developed both the matrix and combinatorial procedures for binding to large numbers of sites. A new, exact, and fast combinatorial procedure is presented. In this procedure the sites may be single or overlapping in a linear lattice or in the form of a ring. The dimensions of the ring of 11 binding sites for L-tryptophan on the trp RNA-binding attenuation protein are such as to prevent direct interactions between the L-tryptophan molecules. Reasonable and explicit assumptions on analyzing the binding data lead to the conclusion that binding of L-tryptophan raises the energy level of (destabilizes) the 11 membered structure.
Saroff
H A
HA
Laboratory of Biochemical Pharmacology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Kiefer
J E
JE
D001426:Bacterial Proteins; D001665:Binding Sites; D007700:Kinetics; D008024:Ligands; D008954:Models, Biological; D011485:Protein Binding; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*; D014364:Tryptophan / Q000378:metabolism*
D001426:Bacterial Proteins; D008024:Ligands; C079092:MtrB protein, Bacteria; D016601:RNA-Binding Proteins; D014157:Transcription Factors; D014364:Tryptophan