Distance and dihedral angle constraints

The solution conformation of plastocyanin from French bean, spinach, and S. obliquus has now been determined from distance and dihedral angle constraints derived by NMR spectroscopy [37,40]. These two-dimensional NMR studies have indicated a well defined backbone conformation, which is very similar to that of poplar PCu in the crystalline state. However, in the case of S. obliquus there are deletions at positions S7 and 58 which influence the shape in the acidic region and in particular close to residues 59-61. The gap which is created is in effect repaired with consequent tightening of the loop 57-62 as indicated in Fig. 5. One of the pronounced bulges at the remote site of poplar and presumably other higher plant plastocyanins is not therefore present in S. obliquus (or plastocyanin from other green algae) [31, 32], as well as parsley... 

Raphson Torsion Angle Minimizer) home.html compatible with distance and dihedral angle constraints obtained typically from nuclear magnetic resonance (NMR) experiments. 

A novel approach based on the application of solid-state NMR spectroscopy has been reported that permits the rapid determination of 3D molecular structure with a single uniformly isotope labelled sample. Analogy with the solution NMR spectroscopic investigations is used, which rely on the detection of short distances between hydrogen atoms providing the principal source of information about the 3D fold of the protein. Since the 2D H, H-correlation methods are of limited use for solid-state NMR spectroscopy due to the restricted spectral resolution, the indirect detection and structural analysis of interactions via C, C-correlation spectroscopy is proposed. It has been shown that combined with dihedral-angle constraints, which can be derived from conformation-dependent chemical shifts, the characterisation of the 3D molecular structure from a single protein sample becomes possible. The new approach has been demonstrated on kaliotoxin, a 38-residue peptide. 

Besides the NOE, the NMR technique offers other information that can also be used in structure determination. Spin-spin coupling constants are a traditional source of such information, and it is becoming increasingly clear that the chemical shifts in proteins and nucleic acids can often give direct information on the secondary and tertiary structure since they depend upon the local environment. This additional NMR information can be used at several levels. Coupling constant information is often converted to dihedral angle constraints and used in a manner similar to the distance constraints derived from NOE information. Because of the complexity of the interactions that influence the chemical shift, this information is more useful at the final structure refinement stage, where the overall structure has already been determined. 

The hypothetical enantiophore queries are constructed from the CSP receptor interaction sites as listed above. They are defined in terms of geometric objects (points, lines, planes, centroids, normal vectors) and constraints (distances, angles, dihedral angles, exclusion sphere) which are directly inferred from projected CSP receptor-site points. For instance, the enantiophore in Fig. 4-7 contains three point attachments obtained by ... 

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