Crystallographic backbone models

The above findings and proposals about the location and function of the Rpb4/7 complex were generally confirmed and extended by recent crystallographic backbone models of the complete Pol II that includes the... 

Fig. 7. A stereodiagram of the conserved iLBP backbone. The conformation of an iLBP may be related to a conserved backbone of residues. The crystallographic Ca model of ALBP is displayed along with the side chains of the conserved residues, which form the hydrophobic core and the adjacent hydrophilic amino acids. For reference to the amino acid sequence, every tenth amino acid is numbered.

The result is the electron density map of the protein crystal. The final task for the crystallographer is to build the appropriate protein model, i. e., putting amino acid for amino acid into the electron density. Routinely the theoretical amplitudes and phases are calculated from the model and compared to the experimental data in order to check the correctness of model building. The positions of the protein backbone and the amino acid side chains are well defined by X-ray structures at a... 

L.133 Using two sets of backbone RDC data, collected in bacteriophage Pfl and bicelle media, they obtained order tensor parameters using a set of crystallographic coordinates for the structural model. This allowed the refinement of C -C bond orientations, which then provided the basis for their quantitative interpretation of C -H RDCs for 38 out of a possible 49 residues in the context of three different models. The three models were (A) a static xi rotameric state (B) gaussian fluctuations about a mean xi torsion and (C) the population of multiple rotameric states. They found that nearly 75% of xi torsions examined could be adequately accounted for by a static model. By contrast, the data for 11 residues were much better fit when jumps between rotamers were permitted (model C). The authors note that relatively small harmonic fluctuations (model B) about the mean rotameric state produces only small effects on measured RDCs. This is supported by their observation that, except for one case, the static model reproduced the data as well as the gaussian fluctuation model. 

RNA and DNA are in general very difficult to model with force-field based approaches. One major difficulty is to reproduce the backbone conformation (crucial for any modeling of nucleic acids), as the corresponding torsional energy barriers are very small [29]. First results from AIMD are encouraging the calculated structure of a hydrated GpG RNA duplex in laboratory realizable conditions (that is, in the crystal phase)[25] showed excellent agreement with experiment and provided the H-bond network postulated by the crystallographers. 

All the ferrichromes whose conformations have been studied are des-scribedin Fig. 1. This structural model is based on the X-ray crystallographic study of ferrichrome A by Zalkin et al. (27, 28) and in most respects, it is confirmed by PMR solution studies (29, 30). The structure exhibited by the model in Fig. 1 is globular with the three substituted ornithyl side chains embracing the metal ion in octahedral coordination while the cyclohexapeptide backbone assumes a distorted antiparallel /3-pleated sheet structure. 

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