J. Gabarro-Arpa

Object Command Language: a formalism to build molecular models and to analyze structural parameters in macromolecules, with applications to nucleic acids

We have written a programming language OCL (Object Command Language) to solve, in a general way, two recurring problems that arise during the construction of molecular models and during the geometrical characterization of macromolecules: how to move precisely and reproducibly any part of a molecular model in any user-defined local reference axes; and how to calculate standard or user-defined structural parameters that characterize the complex geometries of any macromolecule. OCL endows the user with three main capabilities: the definition of subsets of the macromolecule, called objects in OCL, with a formalism from elementary set theory or lexical analysis; the definition of sequences of elementary geometrical operations, called procedures in OCL, enabling one to build arbitrary three-dimensional (3D) orthonormal reference frames, to be associated with previously defined objects; and the transmission of these definitions to programs that allow one to display, to modify and to analyze interactively the molecular structure, or to programs that perform energy minimizations or molecular dynamics. Several applications to nucleic acids are presented.

Binding of Net-Fla, a netropsin-flavin hybrid molecule, to DNA: molecular mechanics and dynamics studies in vacuo and in water solution.

We have studied the binding of the hybrid netropsin-flavin (Net-Fla) molecule onto four sequences containing four A. T base pairs. Molecular mechanics minimizations in vacuo show numerous minimal conformations separated by one base pair. 400 ps molecular dynamics simulations in vacuo have been performed using the lowest minima as the starting conformations. During these simulations, the flavin moiety of the drug makes two hydrogen bonds with an amino group of a neighboring guanine. A 200 ps molecular dynamics simulation in explicit water solution suggests that the binding of Net-Fla upon the DNA substrate is enhanced by water bridges. A water molecule bridging the amidinium of Net-Fla to the N3 atom of an adenine seems to be stuck in the drug-DNA complex during the whole simulation. The fluctuations of the DNA helical parameters and of the torsion angles of the sugar-phosphate backbone are very similar in the simulations in vacuo and in water. The time auto-correlation functions for the DNA helical parameters decrease rapidly in the picosecond range in vacuo. The same functions computed from the water solution molecular dynamics simulations seem to have two modes: the rapid mode is similar to the behavior in vacuo, and is followed by a slower mode in the 10 ps range.

MORMIN: a quasi-Newtonian energy minimizer fitting the nuclear Overhauser data

In this article, we describe the program MORMIN, which can simultaneously minimize the mechanical energy of a given macromolecular structure, together with a weighted quadratic penalty function of the difference between the observed and computed nuclear Overhauser effect (nOe) peaks. The gradient of the nOe penalty function relatively to the proton coordinates is computed from an exact closed formula of a matrix exponential derivative. To cut CPU time, the molecular system is partitioned into nonoverlapping subsets containing the protons involved in the observed peaks. The algorithm is no longer exact, but if a 1% relative error is accepted it can be run, on a scalar computer, in about the same CPU time as needed for the calculation of the mechanical energy. We have successfully run the program in more than 1000 situations, including cases where the hybrid method failed because of the occurrence of negative eigenvalues. In some cases, the optimization of the Cartesian coordinates could be successfully extended to individual atomic diffusion times.

Cadira: an object-oriented platform for modelling molecules and analyzing simulations

Abstract Based on the implementation of a high-level programming language, we have built a software platform which incorporates analysis of molecular simulations, molecular modelling and symbolic calculations.

About the large fluctuations observed using gas-phase molecular dynamics in the K-ras gene containing a mismatch

We describe how we can reduce the periodic bending motions in the simulation in vacuo of the molecular dynamics of a short DNA fragment containing the Gly 12 hot spot of the K-ras oncogene and having at its center a mismatch CA+.