DYNAX: A New System for Biomolecular Dynamics
Simulation in Solution
Atsushi Yoshimori

Carlos A. Del Carpio

yosimori@translell.eco.tut.ac.jp

carlos@translell.eco.tut.ac.jp

Laboratory for Informatics & AI in Molecular and Biological Sciences
Department of Ecological Engineering, Toyohashi University of Technology
Tenpaku, Toyohashi, 441-8580, Japan

1 Introduction
One of the ordinary methods to understand accurately the intermolecular interactions and transition
undergoing in a biomolecule is the dynamics simulations carried out with the assistance of computers.
The advent of more powerful and low cost computers has made this type of simulations routine workand many semiempirical potential functions are being continuously improved in order to reduce evenmore the processing time and express more accurately intermolecular interactions. However many such
simulation systems still oversimplify the interaction of the protein atoms with the solvent. In this work
we have developed a new system for biomolecular dynamics simulation whose main characteristic isthe use of a new potential energy proposed to explicitly take into account the solvent e ect on thestructural characteristics of biomolecules.

2 Solvent E ect
The main characteristics of our potential function are the consideration of the solvent as a continuum
medium, and the computation of the solvent e ect as the sum of two interaction energy terms: (i)A hydrophobic interaction term and (ii) a solute-solvent electrostatic interaction term [1]. The hydrophobic interaction term is calculated as a function of the solvent accessible surface area (SASA)of the protein, while the electrostatic interaction term is computed by means of the generalized Bornequation [2].

3 Dynamics Simulation
Protein dynamics calculates the motion of the atoms in a protein by generating the changes of theatomic coordinates as a function of time. At each time step, new positions and velocities of each of
the atoms are determined by solving the equations of motion using the old positions, the old velocities
and the accelerations, always under the restriction imposed by the law of energy conservation.
To compute new positions, velocities and accelerations of the atoms composing the protein, we use
the elemental Newton equation and the formula proposed by Beeman to solve the resulting di erential
equation [3].
Protein dynamics simulations using the system developed in this work has allowed us to de ne
two new characteristics for polypeptides in function of which particular properties of protein folding
can be expressed. These two characteristics are:(1) The Fluctuating Hydrogen Bond: As e ect of long term dynamics (2 ps) several hydrogen bonds
are broken and new formed, being a characteristic of the particular protein the number of these374

uctuating hydrogen bonds. Furthermore, its calculation is a measure of the stability of adetermined conformer.
(2) The Fluctuating SASA: Dynamic simulations using our system allow the de nition of this newproperty, which is directly related to the solvent pressure on the atoms constituting the protein.
The calculation of the uctuating SASA for regions in the protein allows the computation of auctuating solvent-protein con guration.

4 Results and Discussion
Several properties and new parameters can be obtained by the dynamics simulations of proteins. One
such calculation is the rate of ordering and reordering of the protein in what are called secondary
structure elements of protein structures, ( helices, sheets, coils, etc.). Our system also allows topath the trajectory followed by interprotein segments, such as sense anti-sense peptides, leading to
new insights in the eld of protein engineering and speci cally in protein folding processes.

Figure 1: Dynamics Simulations of BPTI,using Dynax (2ps).

References[1] Del Carpio, C.A. and Gogonea, V., Modelling Proteins Conformation in Solution, Part I:A Parallel
GA Engine for Protein Conformational Space Mapping, Genome Informatics 1996, Universal
Academy Press, 108{118, 1996.
[2] Del Carpio, C.A. , A Parallel Genetic Algorithm for Polypeptide Three Dimensional Structure
Prediction, A Transputer Implementation, J. Chem. Inf. Comput. Sci., 36(2):258{269, 1996.
[3] Beeman, D., Some Multistep Methods for Use in Molecular Dynamics Calculations, J. Comp.
Phy., 20:130{139, 1976.
375