LINCS: A Linear Constraint Solver for Molecular Simulations

In this article we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is 3 to 4 times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. Introduction In classical molecular simulation methods, such as Molecular Dynamics (MD) or Langevin Dynamics (LD), the time step is limited by bond oscillations. These oscillations have a relatively high frequency and low amplitude. By replacing the bond vibrations by holonomic constraints the time step in molecular simulations can be increased by a factor of 4. ..

Relationship between molecular structure and supramolecular morphology of DODA-EO2-biotin and related lipids

We have recently reported that a biotinylated lipid molecule, called DODA-EO2-biotin, forms tubular lipid structures upon hydration, which act as a matrix for the formation of ordered helical arrays of streptavidin as well as for secondary macromolecular recognition reactions involving biotinylated structures (Ringler et al., 1997). In the present study, the supramolecular structures formed by the compounds obtained during the synthesis of DODA-EO2-biotin and of compounds structurally related to DODA-EO2-biotin were investigated by transmission electron microscopy, with the objective being to understand the relationship between molecular structure and supramolecular morphology. From the eight lipid molecules investigated, only DODA-EO2-biotin formed tubular structures. Several structural parameters were identified as playing a role in the formation of DODA-EO2-biotin tubes, such as the chirality of the biotin moiety, the saturated nature of the lipid chains, the presence of amide bonds and the correct length and structure of the hydrophilic spacer. In addition, helical crystals of streptavidin were only obtained upon binding of streptavidin to the supramolecular assemblies formed by DODA-EO2-biotin.