David Bostick

Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl.

Molecular dynamics simulations are performed on two hydrated dipalmitoylphosphatidylcholine bilayer systems: one with pure water and one with added NaCl. Due to the rugged nature of the membrane/electrolyte interface, ion binding to the membrane surface is characterized by the loss of ion hydration. Using this structural characterization, binding of Na(+) and Cl(-) ions to the membrane is observed, although the binding of Cl(-) is seen to be slightly weaker than that of Na(+). Dehydration is seen to occur to a different extent for each type of ion. In addition, the excess binding of Na(+) gives rise to a net positive surface charge density just outside the bilayer. The positive density produces a positive electrostatic potential in this region, whereas the system without salt shows an electrostatic potential of zero.

Complexation of Phosphatidylcholine Lipids with Cholesterol

It is postulated that the specific interactions between cholesterol and lipids in biological membranes are crucial in the formation of complexes leading subsequently to membrane domains (so-called rafts). These interactions are studied in molecular dynamics simulations performed on a dipalmitoylphosphatidylcholine (DPPC)-cholesterol bilayer mixture and a dilauroylphosphatidylcholine (DLPC)-cholesterol bilayer mixture, both having a cholesterol concentration of 40 mol %. Complexation of the simulated phospholipids with cholesterol is observed and visualized, exhibiting 2:1 and 1:1 stoichiometries. The most popular complex is found to be 1:1 in the case of DLPC, whereas the DPPC system carries a larger population of 2:1 complexes. This difference in the observed populations of complexes is shown to be a result of differences in packing geometry and phospholipid conformation due to the differing tail length of the two phosphatidylcholine lipids. Furthermore, aggregation of these complexes appears to form hydrogen-bonded networks in the system containing a mixture of cholesterol and DPPC. The CH...O hydrogen bond plays a crucial role in the formation of these complexes as well as the hydrogen bonded aggregates. The aggregation and extension of such a network implies a possible means by which phospholipid:cholesterol domains form.

An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface

We propose an algorithm for the general description of rugged molecular scale interfacial surfaces. This algorithm was implemented in the description of a phospholipid membrane/water interface with the rugged surface defined by the phospholipid phosphorous atoms. The method allowed us to clearly discern four layered regions of water based upon the water local density as a function of the distance from the membrane surface. Furthermore, the water in each of the layered regions was found to have distinct orientational properties. The classification we make based on density due to our new algorithm is in agreement with that delineated in previous studies based on water orientation. The contribution of the different water regions to the total electrostatic potential reveals the particular way in which each layer’s water polarization contributes to the total dipole potential of the hydrated membrane.

The Implementation of Slab Geometry for Membrane-Channel Molecular Dynamics Simulations

Slab geometric boundary conditions are applied in the molecular dynamics simulation of a simple membrane-channel system. The results of the simulation were compared to those of an analogous system using normal three-dimensional periodic boundary conditions. Analysis of the dynamics and electrostatics of the system show that slab geometric periodicity eliminates the artificial bulk water orientational polarization that is present while using normal three-dimensional periodicity. Furthermore, even though the water occupancy and volume of our simple channel is the same when using either method, the electrostatic properties are considerably different when using slab geometry. In particular, the orientational polarization of water is seen to be different in the interior of the channel. This gives rise to a markedly different electric field within the channel. We discuss the implications of slab geometry for the future simulation of this type of system and for the study of channel transport properties.

A Simple Topological Representation of Protein Structure: Implications for New, Fast, and Robust Structural Classification

A topological representation of proteins is developed that makes use of two metrics: the Euclidean metric for identifying natural nearest neighboring residues via the Delaunay tessellation in Cartesian space and the distance between residues in sequence space. Using this representation, we introduce a quantitative and computationally inexpensive method for the comparison of protein structural topology. The method ultimately results in a numerical score quantifying the distance between proteins in a heuristically defined topological space. The properties of this scoring scheme are investigated and correlated with the standard Cα distance root‐mean‐square deviation measure of protein similarity calculated by rigid body structural alignment. The topological comparison method is shown to have a characteristic dependence on protein conformational differences and secondary structure. This distinctive behavior is also observed in the comparison of proteins within families of structural relatives. The ability of the comparison method to successfully classify proteins into classes, superfamilies, folds, and families that are consistent with standard classification methods, both automated and human‐driven, is demonstrated. Furthermore, it is shown that the scoring method allows for a fine‐grained classification on the family, protein, and species level that agrees very well with currently established phylogenetic hierarchies. This fine classification is achieved without requiring visual inspection of proteins, sequence analysis, or the use of structural superimposition methods. Implications of the method for a fast, automated, topological hierarchical classification of proteins are discussed. Proteins 2004.

A new topological method to measure protein structure similarity

A method for the quantitative evaluation of structural similarity between protein pairs is developed that makes use of a Delaunay-based topological mapping. The result of the mapping is a three-dimensional array which is representative of the global structural topology and whose elements can be used to construe an integral scoring scheme. This scoring scheme was tested for its dependence on the protein length difference in a pairwise comparison, its ability to provide a reasonable means for structural similarity comparison within a family of structural neighbors of similar length, and its sensitivity to the differences in protein conformation. It is shown that such a topological evaluation of similarity is capable of providing insight into these points of interest. Protein structure comparison using the method is computationally efficient and the topological scores, although providing different information about protein similarity, correlate well with the distance root-mean-square deviation values calculated by rigid-body structural alignment.