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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 fold refers to the general protein architecture, like a helix bundle, β-barrel, Rossmann fold or different "folds" provided in the Structural Classification of Proteins database. [11] A related concept is protein topology.
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 ...
Pyruvate kinase, a protein with three domains (In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of ...
The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined).
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.
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.