Simulation of diffusion time of small molecules in protein crystals.
A simple model for evaluation of diffusion times of small molecule into protein crystals has been developed, which takes into account the physical and chemical properties both of protein crystal and the diffusing molecules. The model also includes consideration of binding and the binding affinity of a ligand to the protein. The model has been validated by simulation of experimental set-ups of several examples found in the literature. These experiments cover a wide range of situations: from small to relatively large diffusing molecules, crystals having low, medium, or high protein density, and different size. The reproduced experiments include ligand exchange in protein crystals by soaking techniques. Despite the simplifying assumptions of the model, theoretical and experimental data are in agreement with available data, with experimental diffusion times ranging from a few seconds to several hours. The method has been used successfully for planning intermediate cryotrapping experiments in maltodextrin phosphorylase crystals.
Geremia
Silvano
S
Center of Excellence in Biocrystallography, Department of Chemical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy. geremia@units.it
Campagnolo
Mara
M
Demitri
Nicola
N
Johnson
Louise N
LN
D003198:Computer Simulation; D003460:Crystallization; D004058:Diffusion; D008956:Models, Chemical; D009113:Muramidase / Q000737:chemistry*; D036103:Nanotechnology; D019906:Nuclear Magnetic Resonance, Biomolecular; D011506:Proteins / Q000737:chemistry*
D011506:Proteins; D009113:Muramidase