Beta rotamer

Cannon, in 1975, suggested that dopamine might bind to Its receptors in two possible conformational extremes, which he designated the "alpha" and "beta" rotamers, XIa and Xlb, respectively (20). In this view apomorphine would represent a structure containing a dopamine fragment "frozen" into the alpha rotameric form. By contrast, 6,7-ADTN contains a dopamine moiety constrained in the beta rotameric form. In both cases the side chain is nearly coplanar with the aromatic ring and is... 

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

The two protons on the beta carbon (Cp) are labeled Hpj and Hp2, and the proton on the alpha carbon (CJ is labeled H ,. Although Hpi and Hp2 may at first appear to be identical—especially if we draw the molecule in two dimensions—the three Newman projections showing the rotamers resulting from rotation about the Cp—C , bond reveal that the beta protons do not experience the same chemical environment. 

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