Fragment-base alignment

Fig. 5. Structure-based alignment of the sequences of the water-soluble Rieske fragment from bovine heart bci complex (ISF), the water-soluble Rieske fragment from spinach b f complex (RFS), and of the Rieske domain of naphthalene dioxygenase (NDO) and of the metal binding loops of rubredoxin (RXN) and transcriptional factor TFIIS (TFI). The numbering of the j3 strands is the same for the ISF and RFS. The metal binding ligands are highlighted the asterisks indicate those residues that are fully conserved between the three Rieske proteins.

The problem of constraining relative orientations of protein-fragments based on a single set of residual dipolar couplings has been addressed. A procedure based on order tensor analysis in two alignment media has been suggested and demonstrated for residual dipolar coupling data... 

Figure 15.2 Generalized flow diagram of fragment-based models, (a] Sequence information for PDB ID 4JRC. The sequence is divided into (b] coarse-grained sequence fragments, which are then (c] aligned to a preassembled structure library, (d] The best-fit structures are chosen and then [e] combined and minimized to form (f] the final three-dimensional structure. Disclaimer this diagram is generalized and not comprehensive to all fragment-based models.

Figure 36-25. Double-strand break repair of DNA. The proteins Ku and DNA-dependent protein kinase combine to approximate the two strands and unwind them. The aligned fragments form base pairs the extra ends are removed, probably by a DNA-PK-associated endo- or exonuclease, and the gaps are filled in and continuity is restored by ligation.

---