Figure 5

Heparin prevents domain separation in alkaline pH Time evolution of the distance between the centers-of-mass of each catB domain (L and R) during the MD. The domain nomenclature follows those adopted for papain. The L-domain corresponds to the amino terminus of catB (with exception of the first 10 residues) up to Y148 and the last four carboxy-terminal residues. The R-domain comprises the first 10 residues and the segment that extends from Y148 until the last four residues. Inset: Domain definitions of catB (colored red and blue respectively) were submitted to Domain Select analysis and the main axis of overall movement for apo catB (pH 8) showing the direction of the domain separation effect. We selected for this analysis the starting structure and the average structure of the 40ns MD simulation.