Glycosaminoglycans (GAGs) are important complex carbohydrates that participate in many biological processes through the regulation of their various protein partners. Biochemical, structural biology and molecular modelling approaches have assisted in understanding the molecular basis of such interactions, creating an opportunity to capitalize on the large structural diversity of GAGs in the discovery of new drugs. The complexity of GAG-protein interactions is in part due to the conformational flexibility and underlying sulphation patterns of GAGs, the role of metal ions and the effect of pH on the affinity of binding. Current understanding of the structure of GAGs and their interactions with proteins is here reviewed: the basic structures and functions of GAGs and their proteoglycans, their clinical significance, the three-dimensional features of GAGs, their interactions with proteins and the molecular modelling of heparin binding sites and GAG-protein interactions. This review focuses on some key aspects of GAG structure-function relationships using classical examples that illustrate the specificity of GAG-protein interactions, such as growth factors, anti-thrombin, cytokines and cell adhesion molecules. New approaches to the development of GAG mimetics as possible new glycotherapeutics are also briefly covered. Carbohydrates can exist as simple sugars and as complex conjugates known as glycans. Glycans mediate a wide variety of events in cell-cell and cell-matrix interactions that are crucial to the development and function of complex multicellular organisms. Glycomic technologies for exploring the structure of complex sugar molecules have emerged in the past two decades, opening up a new frontier which has been called 'glycobiology' (1). This review provides an introduction to the structural properties of the linear chain glycans called glycosaminoglycans (GAGs) and their interactions with proteins. Basic Features and Functions of GAGsGlycosaminoglycans are large complex carbohydrate molecules that interact with a wide range of proteins involved in physiological and pathological processes (2,3). Glycosaminoglycans are sometimes known as mucopolysaccharides because of their viscous, lubricating properties, as found in mucous secretions. These molecules are present on all animal cell surfaces in the extracellular matrix (ECM), and some are known to bind and regulate a number of distinct proteins, including chemokines, cytokines, growth factors, morphogens, enzymes and adhesion molecules (2,4). The key properties of GAGs are summarized in Table 1.Glycosaminoglycans in aqueous solution are surrounded by a shell of water molecules, which makes them occupy an enormous hydrodynamic volume in solution (5). When a solution of GAGs is compressed, the water is squeezed out and the GAGs are forced to occupy a smaller volume. When the compression is removed, GAGs regain their original hydrated volume because of the repulsion arising from their negative charges (5). Classification of GAGsGlycosaminoglycans are linear, sulph...

We have performed a multivariate logistic regression analysis to establish a statistical correlation between the structural properties of water molecules in the binding site of a free protein crystal structure, with the probability of observing the water molecules in the same location in the crystal structure of the ligand-complexed form. The temperature B-factor, the solvent-contact surface area, the total hydrogen bond energy and the number of protein-water contacts were found to discriminate between bound and displaceable water molecules in the best regression functions obtained. These functions may be used to identify those bound water molecules that should be included in structure-based drug design and ligand docking algorithms. FIGURE The binding site ( thin sticks) of penicillopepsin (3app) with its crystallographically determined water molecules ( spheres) and superimposed ligand (in thick sticks, from complexed structure 1ppk). Water molecules sterically displaced by the ligand upon complexation are shown in cyan. Bound water molecules are shown in blue. Displaced water molecules are shown in yellow. Water molecules removed from the analysis due to a lack of hydrogen bonds to the protein are shown in white. WaterScore correctly predicted waters in blue as Probability=1 to remain bound and waters in yellow as Probability<1x10(-20) to remain bound.

The presence of water molecules plays an important role in the accuracy of ligand-protein docking predictions. Comprehensive docking simulations have been performed on a large set of ligand-protein complexes whose crystal structures contain water molecules in their binding sites. Only those water molecules found in the immediate vicinity of both the ligand and the protein were considered. We have investigated whether prior optimization of the orientation of water molecules in either the presence or absence of the bound ligand has any effect on the accuracy of docking predictions. We have observed a statistically significant overall increase in accuracy when water molecules are included during docking simulations and have found this to be independent of the method of optimization of the orientation of water molecules. These results confirm the importance of including water molecules whenever possible in a ligand-protein docking simulation. Our findings also reveal that prior optimization of the orientation of water molecules, in the absence of any bound ligand, does not have a detrimental effect on the improved accuracy of ligand-protein docking. This is important, given the use of docking simulations to predict the binding modes of new ligands or drug molecules.

Molecular dynamics simulations have been used to investigate the effect of DMSO on 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) phospholipid bilayers. The concentration of DMSO was varied between 0 and 25.0 mol %. For both lipids, DMSO causes the membrane to expand in the plane of the membrane while thinning normal to that plane. Above a critical concentration, pores in the membrane form spontaneously, and if the concentration is increased further, then the bilayer structure is destroyed. Even at concentrations below those required to induce pores, DMSO readily diffuses across the bilayers. The free-energy profile associated with the diffusion of a DMSO molecules across the membrane has been calculated. The simulations suggest that the DOPC bilayer is more resistant to the deleterious effects of DMSO, both increasing the stability of the membranes and decreasing the rate at which DMSO diffuses across the membrane. In this way, the work highlights the importance of investigating the lipid composition of cell membranes when characterizing the effects of cryosolvents.

Molecular dynamics (MD) simulations have been used to investigate the interactions of a variety of hydroxylated cryosolvents (glycerol, propylene glycol and ethylene glycol), methanol and dimethyl sulfoxide (DMSO) in aqueous solution with a 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) bilayer in its fluid phase at 323K. Each cryosolvent induced lateral expansion of the membrane leading to thinning of the bilayer and resulting in disordering of the lipid hydrocarbon chains. Propylene glycol and DMSO were observed to exhibit a greater disordering effect on the structure of the membrane than the other three alcohols. Closer examination exposed a number of effects on the lipid bilayer as a function of the molecular size and hydrogen bonding capacity of the cryosolvents. Analyses of hydrogen bonds revealed that increased concentrations of the polyhydroxylated cryosolvents induced the formation of a cross-linked cryosolvent layer across the surface of the membrane bilayer. This effect was most pronounced for glycerol at sufficiently high concentrations, which displayed a comparatively enhanced capacity to induce cross-linking of lipid headgroups resulting in the formation of extensive hydrogen bonding bridges and the promotion of a dense cryosolvent layer across the phospholipid bilayer.

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A series of molecular dynamics simulations have been performed on a system comprising 256 water molecules and 1 ethane molecule at 279, 302, 320, and 352 K. The structural analysis revealed the existence of orientational restrictions for water molecules with respect to the solute in the hydration shell, while a hydrogen bond analysis showed a slight enhancement of the tetrahedral network. This behavior is consistent with the negative entropy and enthalpy functions associated with the hydrophobic hydration of nonpolar solutes near room temperature. The dynamical analysis shows that hydration-shell water molecules have slightly lower diffusion coefficients; on the other hand, calculations of hydrogen bond lifetimes reveal that this region's bonding network breaks up faster than that of the bulk. The overall results suggest that the energetic environment in the hydration shell is similar to that in the bulk and reinforce the idea of a reduction in the number of low-energy paths for molecular orientational rearrangements in the vicinity of nonpolar solutes.