Distance and dihedral angle

Figure 3 Model building by Modeller [31], First, spatial restraints in the form of atomic distances and dihedral angles are extracted from the template stmcture(s). The alignment is used to determine equivalent residues between the target and the template. The restraints are combined into an objective function. Finally, the model for the target is optimized until a model that best satisfies the spatial restraints is obtained. This procedure is technically similar to the one used in structure determination by NMR.

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... 

Distance and dihedral angle calculations on triacylglycerol structures using energy minimization molecular modeling approach were able to explain the relative crystallization tendency of vegetable oils in the bent fork conformation (61). 

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

MODELLER [49] builds models of three-dimensional structures of proteins by satisfaction of spatial restraints distances and dihedral angles in the target sequence, stereochemical restraints such as bond length and bond angle obtained from the CHARMM forcefield, and statistical preferences of dihedral angles and non-bonded atomic distances obtained from a representative set of all known protein structures. The model is then calculated by an optimization method relying... 

The dependence of the ( 7r) ( r ) and ( 7r) ( 7r ) surfaces on distance and dihedral angle are displayed in the contour plots shown in Figs. 13.4 and 13.5 respectively. The contour plot in Fig. 13.4 shows a shallow well excimer on the (7r) ( r ) surface at 2.75 A for a wide range of dihedral angles. Indeed this surface... 

Figure 6 Application of the exciton chiraiity method to oligonaphthalenes with two TPPs. The number of naphthalene groups changes the distance and dihedral angle of two TPP groups, which resulted in the change of the magnitude and sign of the exciton CD. The orientation of the electric dipole moment of TPP is shown as double-headed arrows.

To date NMR protein structures have usually been calculated on the basis of interproton distances and dihedral angles derived from NOE and J coupling measurements, respectively. Each structure determination necessitates a large number of sophisticated experiments, so that data acquisition and subsequent analysis may take several months. The value of the solution structure lies in the fact that it provides a starting point for the study of protein/substrate interactions, a knowledge of which may then aid drug design. 

Table 8 Mean values for centroid-centroid (R), offset distances and dihedral angle (a) for Tt...Tt dataset. The standard errors of the mean values are given in parentheses and the number of hydrogen bonds [n] is represented in brackets...

Fig. 2.59. Dependencies of split CD A values on e, interchromophoric distance, and dihedral angle (143, 144)...

The energy, E, specified by this target function includes a chemical description of the protein conformation through the use of a force field, Eforcefieid- The force field potentials are generally much simpler representations of all atom force fields. The distance and dihedral angle restraints appear as weighted penalty, E nmr, terms that should be driven to zero. 

Here distance Edihedrai represent the violation energies based on the distance and dihedral angle restraints, respectively. These functions can take several forms, although a simple square well potential is commonly used. The expressions also include a summation over both upper and lower distance violations for example, Edistance = When considering upper distance re-... 

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