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Concept
Protein dynamics
Summary
Proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s),
and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis.
The study of protein dynamics is most directly concerned with the transitions between these states,
but can also involve the nature and equilibrium populations of the states themselves.
These two perspectives—kinetics and thermodynamics, respectively—can be conceptually synthesized in an "energy landscape" paradigm:
highly populated states and the kinetics of transitions between them can be described by the depths of energy wells and the heights of energy barriers, respectively.
Portions of protein structures often deviate from the equilibrium state.
Some such excursions are harmonic, such as stochastic fluctuations of chemical bonds and bond angles.
Others are anharmonic, such as sidechains that jump between separate discrete energy minima, or rotamers.
Evidence for local flexibility is often obtained from NMR spectroscopy. Flexible and potentially disordered regions of a protein can be detected using the random coil index. Flexibility in folded proteins can be identified by analyzing the spin relaxation of individual atoms in the protein. Flexibility can also be observed in very high-resolution electron density maps produced by X-ray crystallography,
particularly when diffraction data is collected at room temperature instead of the traditional cryogenic temperature (typically near 100 K). Information on the frequency distribution and dynamics of local protein flexibility can be obtained using Raman and optical Kerr-effect spectroscopy as well as anisotropic microspectroscopy in the terahertz frequency domain.
Many residues are in close spatial proximity in protein structures.
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Related concepts (16)
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A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent (due to low sequence similarity). Superfamilies typically contain several protein families which show sequence similarity within each family.
Conformational change
Protein dynamics In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors. A macromolecule is usually flexible and dynamic. Its shape can change in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a conformational change. Factors that may induce such changes include temperature, pH, voltage, light in chromophores, concentration of ions, phosphorylation, or the binding of a ligand.
Nanoscopic scale
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