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A protein usually undergoes reversible structural changes in performing its biological function. The alternative structures of the same protein are referred to as different conformations, and transitions between them are called conformational changes.
Levinthal's paradox is a thought experiment in the field of computational protein structure prediction; protein folding seeks a stable energy configuration. An algorithmic search through all possible conformations to identify the minimum energy configuration (the native state) would take an immense duration; however in reality protein folding happens very quickly, even in the case of the most ...
A change in protein conformation produces a change in the net orientation of the dye relative to the surface plane and therefore the intensity of the second harmonic beam. In a protein sample with a well-defined orientation, the tilt angle of the probe can be quantitatively determined, in real space and real time.
The rough secondary-structure content of a biopolymer (e.g., "this protein is 40% α-helix and 20% β-sheet.") can be estimated spectroscopically. [15] For proteins, a common method is far-ultraviolet (far-UV, 170–250 nm) circular dichroism. A pronounced double minimum at 208 and 222 nm indicate α-helical structure, whereas a single minimum ...
Developed by Koshland, Némethy and Filmer in 1966, the KNF model describes cooperativity as a sequential process, where ligand binding alters the conformation, and thus the affinity, of proximal subunits of the protein, resulting in several different conformations that have varying affinities for a given ligand.
A protein folded into its native state or native conformation typically has a lower Gibbs free energy (a combination of enthalpy and entropy) than the unfolded conformation.A protein will tend towards low-energy conformations, which will determine the protein's fold in the cellular environment.
A network of alternative conformations in catalase (Protein Data Bank code: 1gwe) with diverse properties. Multiple phenomena define the network: van der Waals interactions (blue dots and line segments) between sidechains, a hydrogen bond (dotted green line) through a partial-occupancy water (brown), coupling through the locally mobile backbone (black), and perhaps electrostatic forces between ...
Many proteins can also undergo aggregation and misfolding. For example, prions are stable conformations of proteins which differ from the native folding state. In bovine spongiform encephalopathy, native proteins re-fold into a different stable conformation, which causes fatal amyloid buildup.