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.? ? To establish a scheme where accuracy of the computation can be controlled systematically, we? have proposed a new formulation where the surface charge distribution is used explicitly as? a new variable. The surface charge method has a number of advantages. First, it simplifies the? boundary conditions from two to one when solving the electrostatics problem; second, it reduces? the number of degrees of freedom needed in the calculations; and third, it is applicable to arbitrary? geometrical shapes.
| 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 |
