The glycosaminoglycans, the carbohydrate moieties of proteoglycans, bind to growth factors with a high degree of specificity, and induce growth factor dimerization and interactions with growth factor receptors. These interactions lead to the activation of the kinase domain of the receptor and thereby regulate the growth factor activity. We have used molecular modeling methods to study the modes of binding between heparin or heparan sulfate proteoglycans and bFGF, which lead to cis? or trans?dimerization of bFGF. The trans dimer of bFGF was built based on recently published crystal structure of trans dimer of aFGF. The interactions between heparin and bFGF molecules were analyzed and compared to aFGF dimer as well as to the model of cis dimer of bFGF proposed in our previous studies. There is high similarity between aFGF and bFGF dimers, most of the interactions is through negatively charged sulfate groups, however the protein residues involved in interaction are of different type. The D(II)?D(III) domains of the FGF receptor 1 were modeled based on their homology to the light and heavy chain variable regions of the immunoglobulins of known structures. Two complexes of trans dimer bFGF?heparin?FGFR1 were proposed which comply with the requirement that the FGFR1 is to interact with heparin molecule and the primary and secondary binding sites of bFGF in the complex. In the first proposed complex each FGFR1 molecule interacts only with one protomer of the bFGF dimer, whereas in the second proposed complex each FGFR1 molecule interacts with both bFGF molecules. The structural properties of the proposed models are consistent with the binding mechanism of FGF to its receptor, the receptor dimerization, and the reported site-specific mutagenesis and biochemical cross-linking data.UDP-galactose is a substrate for several enzymes transferring galactose to various sugar acceptors. Crystal structures of two proteins were reported, Galactose-1-phosphate Uridylyltransferase and UDP galactose 4-epimerase, with UDP-galactose co-crystalized. Comparison of 3D structure of UDP galactose revealed different conformation in these two complexes. We have used both, NMR and molecular dynamics simulations, to characterize conformational behavior of UDP-galactose in solution. Several simulations were carried out: in vacuo negatively charged UDP-galactose and UDP-galactose with Na+ ions, and also explicitly solvated UDP-galactose. Chemical shifts and coupling constants of lowest energy conformers were calculated using DFT method and deMon NMR program. This approach enabled us to compare experimental and calculated data directly. The combined NMR and computational study showed that prefered solution conformation of UDP- galactose is similar to that present in UDP-galactose?Galactose-1- phosphate Uridylyltransferase complex. The study provides valuable information not only about sugar-nucleotide conformation in solution, but also important information needed for subsequent studies of sugar- protein interactions involving UDP-galactose. 1) Lam et al. J. Biomol. Str. & Dyn. 15: 1009-1027, 1998.2) Rao et al. Int. J. Biol. Macromol. Mol. 23: 295-307, 1998. Z01 BC 10041-04 - computer modeling, Conformation, molecular dynamics, Oligosaccharide, protein carbohydrate interactions,
| Schuyler, Adam D; Jernigan, Robert L; Qasba, Pradman K et al. (2009) Iterative cluster-NMA: A tool for generating conformational transitions in proteins. Proteins 74:760-76 |
