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A part of F1 ATP synthase complex: alpha, beta and gamma subunits (The alpha and beta (or A and B) subunits are found in the F1, V1, and A1 complexes of F-, V- and A-ATPases, respectively, as well as flagellar (T3SS) ATPase and the termination factor Rho. The subunits make up a ring that contains the ATP-hydrolyzing (or producing) catalytic core.
Binding-mode – orientation of the two binding partners relative to each other in the complex The above information yields the three-dimensional structure of the complex. Based on this structure, the scoring function can then estimate the strength of the association between the two molecules in the complex using one of the methods outlined below.
Subunits α and β make a hexamer with 6 binding sites. Three of them are catalytically inactive and they bind ADP. Three other subunits catalyze the ATP synthesis. The other F 1 subunits γ, δ, and ε are a part of a rotational motor mechanism (rotor/axle). The γ subunit allows β to go through conformational changes (i.e., closed, half open ...
In F-ATPases, the flux of protons through the ATPase channel drives the rotation of the C subunit ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the C subunit ring of Fo.
The two binding motifs that ATP directly interacts with is the residues from the Walker A motif, located on one of the subunits, and the residues from the C binding motif, located on the other subunit. The Walker A binding motif has a lysine side chain, which is essential for the binding of ATP. The lysine residue forms hydrogen bonds with the ...
In virtually every case, competitive inhibitors bind in the same binding site (active site) as the substrate, but same-site binding is not a requirement. A competitive inhibitor could bind to an allosteric site of the free enzyme and prevent substrate binding, as long as it does not bind to the allosteric site when the substrate is bound.
There are several types of antibodies and antigens, and each antibody is capable of binding only to a specific antigen. The specificity of the binding is due to specific chemical constitution of each antibody. The antigenic determinant or epitope is recognized by the paratope of the antibody, situated at the variable region of the polypeptide ...
C1q can also be activated in other ways, for example by binding to pentraxins such as C-reactive protein [2] or directly to the surface of pathogens. [1] Such binding of C1q leads to conformational changes in the C1q molecule, which activates the associated C1r molecules. Active C1r cleaves the C1s molecules, activating them.