Protein-water contact

Baker et al. (1987, 1988) described a 1.5 A resoludon structure of 2Zn-insulin. They located 282 of the estimated 285 waters per insulin dimer in the crystal. These were distributed among 349 sites 217 of occupancy 1.0 126 of occupancy 0.5 five of occupancy 0.33 and one of occupancy 0.25. There was evidence for ordered water at a distance 8 A from the protein surface. Nearly 100 waters were bonded only to other waters. The extent of order of the water, judged by B values, increased with an increased number of interactions with the protein. The waters bonded to the protein act as anchors for chains of less well-ordered waters, which are often linked by threads of density, possibly representing paths along which the less-ordered waters are found. There were alternate water positions, sometimes collected into networks of partially occupied sites. Cyclic water structures were found. The protein—water contacts showed preferred geometries. Baker et al. (1988) gave particularly elegant descriptions of the crystal water. 

A model for a hydrated powder of MBP was constructed based on a crystal structure (PDB entry 1JW4 [20]). The model contained four protein molecules generated from four unit cells (a 2a x 2b x c lattice) of the triclinic crystal with the water molecules removed. A large box of water molecules was overlaid on the protein supercell, and all but the 3460 water molecules that were closest to the protein molecules were removed to give h = 0.43, corresponding to samples used in neutron scattering experiments carried out in conjunction with the simulations [8]. A constant pressure and temperature MD simulation at 1 atm and 300 K was used to allow the cell to collapse and anneal the protein-protein and protein-water contacts. A series of production runs were performed at constant pressure over a range of temperature. 

Problems of desorption and loss of activity encountered with natural heparin have led numerous workers to explore synthetic heparin-like polymers or heparinoids, as reviewed by Gebelein and Murphy [475, 514, 515]. The blood compatibility of 5% blended polyelectrolyte/polyfvinly alcohol) membranes was studied by Aleyamma and Sharma [516,517]. The membranes were modified with synthetic heparinoid polyelectrolytes, and surface properties (platelet adhesion, water contact angle, protein adsorption) and bulk properties such as permeability and mechanical characteristics were evaluated. The blended membrane had a lower tendency to adhere platelets than standard cellulose membranes and were useful as dialysis grade materials. 

Hydration water molecules indicate substrate-binding sites. In crystal structures of native proteins, the active sites are usually hydrated if they are not in direct contact with symmetry-related protein molecules. Since the substrates or inhibitors are recognized by the protein and bound to its active site by hydrogen bonds and/or by insertion of hydrophobic residues into hydrophobic pockets, it is not surprising to find, in the native protein, water associated in positions which are the... 

Proteins are crystallized from aqueous solutions using methods that have been extensively studied for simpler molecules and salts (Rosen-berger, 1986 Feigelson, 1988). Despite similar underlying physical principles, protein and small-molecule crystallizations differ in many respects. Unlike the crystallization of simpler molecules, in which solvent is effectively excluded from the crystal, substantial numbers of solvent molecules are immobilized and become ordered at protein lattice contacts, although otherwise protein crystals have large cavities containing essentially liquid water. 

Fig. 14.1 Scheme and plots illustrating the dependence of nanoscale-confinement parameters T and/on the radius 6 of the osculating sphere at the protein-water interface. First-order contacts with a polar or nonpolar patch on the protein surface are treated individually. Values were determined at equilibrium obtained by integrating Newton s equations of motion in an NPT ensemble with box size 103 nm3, starting with the PDB structure embedded in a pre-equilibrated cell of water molecules. The box size was calibrated so that the solvation shell extended at least 10 A from the protein surface at all times. Simulations were performed as described in Chap. 4... 

The folding of a polypeptide chain depends not only on its amino acid sequence but also on the nature of the solvent. Discuss the types of interactions that might occur between water molecules and the amino acid residues of the polypeptide chain. Which groups would be exposed on the exterior of the protein in contact with water and which groups would be buried in the interior of the protein ... 

However, in spite of these similarities, the adsorbed amounts and the structure of the adsorbed mucin and collagen layers on the surfaces studied are entirely different. The behavior of these proteins is analyzed here on the hydrophobic polyethylene surface (water contact angle 0 20 95°), on the surface modified polyethy-lenes oxidized polyethylene (0h q 74°) and poly(maleic acid) grafted polyethylene ( Ho0 74°) a d on the hydrophilic mica surface ( H2 0 0°) Acidic pH = 2.75 (for collagen) and slightly alkaline pH = 7.2 (for mucin) were chosen in order to minimize the association of these proteins in solution and to make possible the analysis of their adsorbabilities in comparable conditions. 

Because of its low wettabihty (and high water contact angle), a substrate with a low surface energy could interact neither with biomolecules nor with water molecules. There is no alBnity, only electrostatic repulsion of the proteins. Hence, the organization of the biomolecules at the interface is not uniform, and cell aggregates are formed. 

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