Computer simulation of aqueous biomolecular systems

A stepwise docking molecular dynamics approach for simulating antibody recognition with substantial conformational changes

Conformational changes or rearrangements are common events during inter-biomolecular recognition. Tracking these changes are essential for exploring the allosteric mechanism and it is usually achieved by molecular dynamics simulation in silico. We previously identified a broad-neutralizing antibody against H5 influenza virus, 13D4, and solved the crystal structures of the free 13D4 Fab and its complex with hemagglutinin (HA). Structural comparison of the unbound and bound 13D4 Fabs showed that the heavy chain complementarity-determining region 3 (HCDR3) undergoes a substantial conformational rearrangement when it recognizes the receptor-binding site (RBS). Here, we used molecular dynamics (MD) to simulate the conformational changes that occur during antibody recognition. We showed that neither conventional MD nor steered MD could recapitulate the loop fitting of the RBS structure contour. Consequently, to simulate these challenging conformational changes, we engaged a stepwise docking MD method that allowed for the gradual docking of the ligand to receptor. This new method recapitulates the bound shape of the HCDR3 and provides the best approximation of the shape rendered by the co-crystal structure, with an RMSD of 0.926 Å. This strategy affords a flexible MD approach for simulating complicated conformational changes that occur during molecular recognition, and helps to provide an understanding of the involved allosteric mechanism.

Comparative studies of high resolution Z-DNA crystal structures. Part 1: Common hydration patterns of alternating dC-dG

The water structure in three crystal forms of the left-handed Z-DNA hexamer [d(CGCGCG)]2 has been analyzed. Several common motifs have been found in the first hydration shells. On the convex surface, the major groove of the left-handed conformation, water molecules bridge the guanine O-6 keto groups at GpC steps. Cytosine N-4 nitrogens of opposite strands are hydrated by tandem water molecules. At the bottom of the minor groove, a string of water molecules connects the cytosine O-2 keto groups. Across the minor groove guanine N-2 nitrogens are bridged to phosphate oxygens of cytosine and guanine residues by one or two water molecules. In contrast to the very regular geometry of the water structure around the bases, the arrangement of water molecules between phosphate groups appears to be less ordered. However, there is a strong correlation between the interphosphate distances and the number of water molecules or ions which link the phosphate groups. In all three structures various ions, such as sodium and magnesium ions, as well as the protonated amino and imino groups of the polycation spermine displace and replace water molecules in the first hydration shell. Nevertheless, the analysis reveals that numerous first hydration shell water molecules in Z-DNA crystals can be regarded as part of the DNA structure. Their positions and thermal parameters are generally independent of changes in the local crystallographic environment.

A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins

The structure and activity of a protein molecule are strongly influenced by the extent of hydration of its cavities. This is, in turn, related to the free energy change on transfer of a water molecule from bulk solvent into a cavity. Such free energy changes have been calculated for two cavities in a sulfate-binding protein. One of these cavities contains a crystallographically observed water molecule while the other does not. Thermodynamic integration and perturbation methods were used to calculate free energies of hydration for each of the cavities from molecular dynamics simulations of two separate events: the removal of a water molecule from pure water, and the introduction of a water molecule into each protein cavity. From the simulations for the pure water system, the excess chemical potential of water was computed to be -6.4 +/- 0.4 kcal/mol, in accord with experiment and with other recent theoretical calculations. For the protein cavity containing an experimentally observed water molecule, the free energy change on hydrating it with one water molecule was calculated as -10.0 +/- 1.3 kcal/mol, indicating the high probability that this cavity is occupied by a water molecule. By contrast, for the cavity in which no water molecules were experimentally observed, the free energy change on hydrating it with one water molecule was calculated as 0.2 +/- 1.5 kcal/mol, indicating its low occupancy by water. The agreement of these results with experiment suggests that thermodynamic simulation methods may become useful for the prediction and analysis of internal hydration in proteins.

Distributions of water around amino acid residues in proteins

The atomic co-ordinates from 16 high-resolution (less than or equal to 1.7 A = 0.1 nm), non-homologous proteins have been used to study the distributions of water molecule sites around the 20 different amino acid residues. The proportion of residues whose main-chain atoms are in contact with water molecules was fairly constant (between 40% and 60%), irrespective of the nature of the side-chain. However, the proportion of residues whose side-chain atoms were in contact with water molecules showed a clear (inverse) correlation with the hydrophobicity of the residue, being as low as 14% for leucine and isoleucine but greater than 80% for asparagine and arginine. Despite the problems in determining accurate water molecule sites from X-ray diffraction data and the complexity of the protein surface, distinct non-random distributions of water molecules were found. These hydration patterns are consistent with the expected stereochemistry of the potential hydrogen-bonding sites on the polar side-chains. The water molecules around apolar side-chains lie predominantly at van der Waals' contact distances, but most of these have a primary, shorter contact with a neighbouring polar atom. Further analysis of these distributions, combined with energy minimization techniques, should lead to improved modelling of protein structures, including their primary shells of hydration.

Water structure in vitamin B12 coenzyme crystals. I. Analysis of the neutron and x-ray solvent densities

The disordered solvent distribution in crystals of vitamin B12 coenzyme was examined using the methods of high-resolution neutron and x-ray diffraction. One set of neutron (0.95 A) and two sets of x-ray (0.94 and 1.1 A) data were collected and the resulting models were extensively refined using least-squares and Fourier syntheses. The solvent regions were analyzed in two stages: first, main sites were assigned to the well defined regions of solvent density and refined using least squares; second, continuous sites were assigned representing the more disordered diffuse and elongated regions of solvent density. During the analysis an acetone molecule was also located. Water networks were formulated from the assigned sites in the above models and also from those assigned in the original structure determination (Lenhert, 1968), using criteria that included hydrogen bonding (derived from small crystal hydrates), van der Waals contact distances, side-chain disorder, water molecule orientations, and the presence or absence of foreign solvent. The well established networks extend throughout all the solvent regions of the crystal with interesting orientational arrangements of the individual waters around both polar and apolar groups of the coenzyme molecule. The networks were seen to be consistent among each of the four models in terms of occupying relatively similar positions. However, the occupancy values of the individual networks varied between the models; some networks were clearly visible in one but attenuated in another. The specific details of the water structure (bonding geometries, short-range nonbonded contacts, orientations of the waters, polar and apolar interactions, etc.) are described in the following paper.