Sialoadhesin-Sialyl Lactose Complex

Calciflations were performed using the crystallographic structure of the sialyl lactose-sialoadhesin complex, PDB crystal structure entry IQFO [64]. 

Since the protein signals at 0 ppm were irradiated for the STD experiment, we made the reasonable assumption that the Leu, Val and He methyl protons were instantaneously saturated. From the intensity matrix I(t), the fractional intensity changes for different ligand protons k were calculated, and compared to the experimental STD values using an NOE R-factor Eq. 6. The value of Wk was assumed to be 1. 

The multilevel coordinate search (MGS) method was used to optimize parameters to get best fit between the experimental and predicted intensities. The NOE R-factor was used as the energy function to be minimized. A version of the MGS method was written based on the version presented by Huyer and Neumaier [65]. The algorithm performs the minimization by a standard coordinate search method. The method was carefully tested by the use of different starting points for the coordinate search and using simulated data sets. This alleviates local minima trapping by MGS, and identifies fhe global minimum within the parameter ranges used in the optimization. 

From the GORGEMA-STD predictions based on the crystal structure, all protons in N-acetyl neuraminic acid and galactose show reasonable STD 

Considering an estimated experimental error of 10-20% for the STD data as well as some systematic errors in the estimates from resonance overlap, the analysis suggests a generally reasonable correspondence between the crystal structure and the solution state. At the same time, our data suggest that the crystallographic structure of the complex may not be entirely compatible 

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Fig. 7 Comparison of experimental and predicted STD values from CORCEMA-ST protocol for the crystal structure of sialoadhesin-sialyl lactose complex at protein/ligand ratio of 1 300. Reprinted from [63] 2004, with permission from Elsevier...

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