Conformational ensembles
computational models of intrinsically-disordered proteins
In protein chemistry, conformational ensembles, also known as structural ensembles, are models describing the structure of intrinsically unstructured proteins. Such proteins are flexible in nature and cannot be described by a single structural representation. The techniques of ensemble calculation are relatively new on the field of structural biology, and are still facing certain limitations that need to be addressed before it will become comparable to classical structural description methods such as biological macromolecular crystallography.
Purpose
Ensembles are models consisting of a set of conformations that describe the structure of a flexible protein. Even though the degree of conformational freedom is extremely high, flexible/disordered protein generally differ from fully random coil structures. The main purpose of these models is to gain insights regarding the function of the flexible protein, extending the structure-function paradigm from folded proteins to intrinsically disordered proteins.
Calculation techniques
The calculation of ensembles rely on experimental measurements, mostly by Neutron spin echo spectroscopy, Nuclear Magnetic Resonance spectroscopy and Small-angle X-ray scattering. These measurements yield structural information.
Short-range
Chemical Shifts (CS)
Residual Dipolar Couplings (RDCs)
J-couplings
Hydrogen-exchange
Solvent-accessibility.
Long-range
Paramagnetic Relaxation Enhancements (PREs)
Nuclear Overhauser effects (NOEs)
SAXS topological restraints.
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