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Protein side chains exhibit rotamers, whose distribution is determined by their steric interaction with different conformations of the backbone. This effect is evident from statistical analysis of the conformations of protein side chains in the Backbone-dependent rotamer library .
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.
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.
Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organization of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure ...
One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein (as at top right). A second is to show the empirical distribution of datapoints observed in a single structure (as at right, here) in usage for structure validation , or else in a database of many structures (as ...
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 ...
This movie depicts the 3-D structures of each of the representative conformations of the Markov State Model of Pin1 WW domain. In computational chemistry, conformational ensembles, also known as structural ensembles, are experimentally constrained computational models describing the structure of intrinsically unstructured proteins.
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 ...