Multiscale Molecular Dynamics of Protein Aggregation

Cesar      L. Avila; Nils      J. D. Drechsel; Raul      Alcantara; Jordi      Villa-Freixa

doi:10.2174/138920311795860205

Abstract

The 60s gave birth to the practical implementation of classical mechanics to unravel the dynamics and energetics of biomolecules. In the 70s the use of generalized force fields and more advanced integrative solutions to the microscopic understanding of nature (like hybrid QM/MM) were introduced. During the 80s, algorithms to obtain free energy values were further developed and in the 90s practical integration schemes of molecular mechanics force fields with other levels of detail (QM on one extreme and advances in implicit solvation on the other) were implemented in widely spread software. In the first decade of the XXIst century a considerable effort has been put in two seemingly discordant models for the simulation of biomolecules. On the one hand, extraordinary advances in computing technologies (both in terms of processor power and of new efficient parallel and distributed computing schemas) have allowed researchers to deal with bigger systems and longer simulations, reaching molecular processes including millions of particles or lying in the milisecond scale. On the other hand, the realization that the relevant answers to many biomolecular problems are not homogeneously distributed through the molecular structure, something already envisioned by the QM/MM pioneers more than three decades ago, has led researchers to find smart ways of putting different emphases on different ranges of the spatial or system time scale. In this context, e.g., molecular aggregation represents a paradigm for multiscalability, as molecular recognition can be understood with simple (semi-)macroscopic electrostatic terms when the two fragments are far apart, while the atomic interactions need to be considered in full detail upon close distances. In this manuscript the current status of the techniques that use multiple scale representations of biomolecules are reviewed, and the findings are synthesized in a modular schema that can be extensively used when studying aggregation processes. It is shown that a smart alternative to brute force and massive computation of uninteresting regions in the all atom potential energy surface is the consideration of a simplified reference potential, explored thoroughly in the relevant regions, combined with a free energy perturbation approach that transforms this simple representation to a full atom representation.

Keywords: Multiscale stimulations, free energy perturbations, coarse grain, classical mechanics, algorithms, molecular structure, Moore's law, low-cost implementation, GPU programming paradigm, technological explosion, Biomedical Information Science, Technology Initiative, graphical cards