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The Hill equation reflects the occupancy of macromolecules: the fraction that is saturated or bound by the ligand. [1] [2] [nb 1] This equation is formally equivalent to the Langmuir isotherm. [3] Conversely, the Hill equation proper reflects the cellular or tissue response to the ligand: the physiological output of the system, such as muscle ...
The first description of cooperative binding to a multi-site protein was developed by A.V. Hill. [4] Drawing on observations of oxygen binding to hemoglobin and the idea that cooperativity arose from the aggregation of hemoglobin molecules, each one binding one oxygen molecule, Hill suggested a phenomenological equation that has since been named after him:
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A protein–ligand complex is a complex of a protein bound with a ligand [2] that is formed following molecular recognition between proteins that interact with each other or with other molecules. Formation of a protein-ligand complex is based on molecular recognition between biological macromolecules and ligands, where ligand means any molecule ...
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Protein tertiary structure – arrangement of the protein atoms in three-dimensional space. Protein structures may be determined by experimental techniques such as X-ray crystallography or solution phase NMR methods or predicted by homology modelling. Ligand active conformation – three-dimensional shape of the ligand when bound to the protein
The comparison of the open and closed structures of CYP2B4 structures reveals large-scale conformational rearrangement between the two states, with the greatest conformational change around the residues 215-225, which is widely open in ligand-free state and shut after ligand binding; and the region around loop C near the heme.
The sequential model (also known as the KNF model) is a theory that describes cooperativity of protein subunits. [1] It postulates that a protein's conformation changes with each binding of a ligand, thus sequentially changing its affinity for the ligand at neighboring binding sites.