Better computer modeling provides a new look at large biomolecules

A new method for studying the electrical landscape of large biological molecules may enable researchers to make a leap from modeling molecules of 50,000 atoms to those of more than a million atoms.

The technique, developed by Howard Hughes Medical Institute (HHMI) researchers at the University of California, San Diego (UCSD), was used to model the electrostatic properties of microtubules, which are part of the cell's structural and transport systems, and ribosomes, which are the cell's protein-making factories. The scientists say their new computer modeling method, called parallel focusing, will provide molecular biologists with a useful tool for exploring the dynamic behavior of complex biomolecules. The scientists plan to make their software widely available to the scientific community.

Electrostatic models portray how the charges on individual atoms of a molecule interact to produce a distribution of electric fields throughout the molecule. Such models have proven useful in analyzing the stability and dynamic motions of biological molecules such as proteins, DNA, RNA and ligands, as well as how they interact.

In an article published online on August 21, 2001, in Proceedings of the National Academy of Sciences, researchers led by HHMI investigator J. Andrew McCammon report that parallel focusing is a new approach to solving the Poisson-Boltzmann equation (PBE), a fundamental equation in the field of electrostatics.

"One of the problems with traditional molecular dynamics methods for simulating large systems, is that they require considerable computational effort to simulate the surrounding atoms of the aqueous solvent," said McCammon. "The Poisson-Boltzmann equation circumvents this by treating the solvent as one featureless polarizable medium -- essentially a big cloud of charge around a molecule such as a protein," he said.

According to McCammon, the effectiveness of the PBE, which is called an "implicit solvent method

Contact: Jim Keeley
Howard Hughes Medical Institute

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