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A typical aptamer is a synthetically generated ligand exploiting the combinatorial diversity of DNA, RNA, XNA, or peptide to achieve strong, specific binding for a particular target molecule or family of target molecules.
An ATP-binding motif is a 250-residue sequence within an ATP-binding protein’s primary structure. The binding motif is associated with a protein’s structure and/or function. [ 1 ] ATP is a molecule of energy, and can be a coenzyme, involved in a number of biological reactions.
The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. [1] [2] [3] ABC transporters belong to translocases.
The aptamer HD22 (also known as HTDQ) is an optimized aptamer with 29 (5 '-AGTCCGTGGTAGGGCAGGTTGGGGTGACT-3 ') or 27 (lacking the first and the last nucleotides of 29-mer form) nucleotides. [2] [18] This aptamer recognizes the exosite II of thrombin, which is involved in the activation of factor V and factor VIII and mediates the heparin binding ...
Clinical uses of the technique are suggested by aptamers that bind tumor markers, [50] GFP-related fluorophores, [51] and a VEGF-binding aptamer trade-named Macugen has been approved by the FDA for treatment of macular degeneration. [44] [52] Additionally, SELEX has been utilized to obtain highly specific catalytic DNA or DNAzymes.
The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q ...
The binding pocket, conserved throughout most isoforms, mostly consists of basic residues that allow for strong binding to ATP or ADP and has a maximal diameter of 20 Å and a depth of 30 Å. [8] Indeed, arginine residues 96, 204, 252, 253, and 294, as well as lysine 38, have been shown to be essential for transporter activity. [13]
Though the γ-subunit can bind AMP/ADP/ATP, only the binding of AMP/ADP results in a conformational shift of the enzyme protein. This variance in AMP/ADP versus ATP binding leads to a shift in the dephosphorylation state for the enzyme. [13] The dephosphorylation of AMPK through various protein phosphatases completely inactivates catalytic ...