Biomolecular interactions determine how transcription? factors recognize their DNA binding? sites, how proteins interact with each other, and? consequently how a biological system functions.? Since many biological molecules bear considerable? electric charge, electrostatic interactions are? among the most important when studying biomolecular? interactions. However, electrostatic? interactions in biological systems are difficult? to calculate accurately in practice. Aside from? the significants charges carried by biomolecules? such as DNA and proteins, the solvent itself ? namely, water produces considerable electrostatic? effects. Furthermore, hydrogen bonds, known to? be involved in helix formation in both DNA and? proteins, are essentially electrostatic in origin.? Indeed, it seems that electrostatic effects often? drive the physical-chemical processes in biological? systems and, thereby, determine biological? function. Therefore, any attempt to perform? molecular dynamics (MD) simulations of biological? systems will require an adequate description? of these electrostatic forces.? ? In the past, we developed a controllable scheme for computing the electrostatic energy.? In principle, one may take the numerical derivative to obtain the electrostatic force.? In reality, the numerical derivative computations are expensive and may become even more? expensive when a high degree of accuracy is demanded. In order to have a practical system for? simulation of biomolecular systems, it becomes necessary to calculate the electrostatic forces? by function evaluation of analytical formulae, which is one of the primary efforts of this ? fiscal year. In the process of doing this, we have also implemented a more stable method for ? evaluating mathematical functions in a rotated coordinate system.? ? We have also developed a new approach that allows for exact calculation of energetics even? if the dielectric constant changes in space in a continuous fashion. This scenario is applicable to the the context, for example, of water layer around biomolecules. To the best of our knowledge, our method is the only one that uses energetic functional in a throughout consistent manner. We? are currently in the process of writing up this result.
| Stojmirovi?, Aleksandar; Yu, Yi-Kuo (2009) Geometric aspects of biological sequence comparison. J Comput Biol 16:579-610 |
| Sardiu, Mihaela E; Cheung, Margaret S; Yu, Yi-Kuo (2007) Cysteine-cysteine contact preference leads to target-focusing in protein folding. Biophys J 93:938-51 |
| Doerr, T P; Yu, Yi-Kuo (2006) Electrostatics of charged dielectric spheres with application to biological systems. Phys Rev E Stat Nonlin Soft Matter Phys 73:061902 |
