Trypsin, molecular surfaces

C. Application Topographical Analysis of the Molecular Surfaces of the Proteins Trypsin and Trypsinogen... 

In Fig. 1 we show an electrostatic potential molecular surface view of the active site of trypsin and of trypsin inhibitor [25]. The complementarity of the electrostatic potentials (blue = positive red = negative) is apparent for the orientation shown here. 

Fig. I. An electrostatic potential molecular surface for the trypsin active site and for trypsin inhibitor [25].

Immobile trypsin-Sepharose and anti-small subunits IgG-Sepharose can fully interact with the large subunits, but not the small subunits, because the long COOH-terminal extensions of the large subunits run between and above small subunits. The small subunits appear largely covered by the large subunits. Perhaps the carboxyl-terminal tail of the small subunit is slightly exposed to the molecular surface, so the small subunits separated from the large subunit core can enter into solution when immobile holoenzyme is dissociated by 2 M urea. 

Figure 17 Molecular surfaces of the enzyme trypsin. The surfiices are color coded according to the molecular lipophilicity (left) calculated by an extended Crippen approach by Heiden et al. " and the electrostatic potential (right) calculated by a finite differences algorithm solving the Poisson-Boltzmann equation. " " Left blue, almost hydrophilic red, almost lipophilic. Right blue, negative gray, neutral red, positive...

Figure 18 Molecular surfaces of the enzyme trypsin. The surfaces are color coded according to the surface topography index (left) and the hydrogen bonding ability (right). Left blue, bag green, saddle red, knob. Right blue, acceptor red, donor...

Trypsin in aqueous solution has been studied by a simulation with the conventional periodic boundary molecular dynamics method and an NVT ensemble.312 340 A total of 4785 water molecules were included to obtain a solvation shell four to five water molecules thick in the periodic box the analysis period was 20 ps after an equilibration period of 20 ps at 285 K. The diffusion coefficient for the water, averaged over all molecules, was 3.8 X 10-5 cm2/s. This value is essentially the same as that for pure water simulated with the same SPC model,341 3.6 X 10-5 cm2/s at 300 K. However, the solvent mobility was found to be strongly dependent on the distance from the protein. This is illustrated in Fig. 47, where the mean diffusion coefficient is plotted versus the distance of water molecules from the closest protein atom in the starting configuration the diffusion coefficient at the protein surface is less than half that of the bulk result. The earlier simulations of BPTI in a van der Waals solvent showed similar, though less dramatic behavior 193 i.e., the solvent molecules in the first and second solvation layers had diffusion coefficients equal to 74% and 90% of the bulk value. A corresponding reduction in solvent mobility is observed for water surrounding small biopolymers.163 Thus it... 

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