Oligosaccharide Conformations and Their Interactions with Proteins

糖胺聚糖，蛋白聚糖的碳水化合物部分，以高度特异性结合生长因子，并诱导生长因子二聚化和与生长因子受体的相互作用。这些相互作用导致受体激酶结构域的活化，从而调节生长因子活性。我们已经使用分子建模方法来研究肝素或硫酸乙酰肝素蛋白多糖和bFGF之间的结合模式，这导致顺式？还是变性人bFGF的二聚化。根据最近发表的aFGF反式二聚体的晶体结构，构建了bFGF的反式二聚体。分析了肝素与bFGF分子之间的相互作用，并与aFGF二聚体以及我们以前提出的bFGF顺式二聚体模型进行了比较。aFGF和bFGF二聚体之间具有高度的相似性，大多数相互作用是通过带负电荷的硫酸基团，但是参与相互作用的蛋白质残基是不同类型的。D（II）？FGF受体1的D（III）结构域基于其与已知结构的免疫球蛋白的轻链和重链可变区的同源性建模。反式二聚体bFGF的两个复合物？肝素？FGFR 1与肝素分子及复合物中bFGF的一级和二级结合位点相互作用。在第一个提出的复合物中，每个FGFR 1分子仅与bFGF二聚体的一个原体相互作用，而在第二个提出的复合物中，每个FGFR 1分子与两个bFGF分子相互作用。所提出的模型的结构特性与FGF与其受体的结合机制、受体二聚化以及已报道的定点突变和生化交联数据相一致。UDP-半乳糖是几种酶将半乳糖转移到各种糖受体的底物。报道了两种蛋白质的晶体结构，半乳糖-1-磷酸尿苷酰转移酶和UDP半乳糖4-差向异构酶，UDP-半乳糖共结晶。UDP半乳糖的三维结构的比较显示，在这两个复合物的不同构象。我们使用NMR和分子动力学模拟来表征UDP-半乳糖在溶液中的构象行为。进行了几次模拟：在真空中带负电荷的UDP-半乳糖和具有Na+离子的UDP-半乳糖，以及明确溶剂化的UDP-半乳糖。用密度泛函方法和deMon核磁共振程序计算了最低能量构象的化学位移和偶合常数。这种方法使我们能够直接比较实验和计算数据。结合NMR和计算研究表明，UDP-半乳糖的优先溶液构象是类似的UDP-半乳糖？半乳糖-1-磷酸尿苷酰转移酶复合物。该研究不仅提供了有价值的信息在溶液中的糖-核苷酸构象，但也为后续研究所需的糖-蛋白质相互作用的UDP-半乳糖的重要信息。1)Lam等人J. Biomol. Str. & Dyn. 15：1009-1027，1998.2）Rao等人，Int. J. Biol. Macromol.摩尔23：295-307，1998. Z 01 BC 10041-04 -计算机建模，构象，分子动力学，寡糖，蛋白质碳水化合物相互作用，

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,