Physical Foundation of Biomolecular Interactions

National Library Of Medicine

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Abstract

Biomolecular interactions determine how transcription factors recognize their DNA binding[unreadable] sites, how proteins interact with each other, and consequently how a biological system functions.[unreadable] Since many biological molecules bear considerable electric charge, electrostatic interactions are[unreadable] among the most important when studying biomolecular interactions. However, electrostatic[unreadable] interactions in biological systems are difficult to calculate accurately in practice. Aside from[unreadable] the significants charges carried by biomolecules such as DNA and proteins, the solvent itself ?[unreadable] namely, water? produces considerable electrostatic effects. Furthermore, hydrogen bonds, known to[unreadable] be involved in helix formation in both DNA and proteins, are essentially electrostatic in origin.[unreadable] Indeed, it seems that electrostatic effects often drive the physical-chemical processes in biological[unreadable] systems and, thereby, determine biological function. Therefore, any attempt to perform[unreadable] molecular dynamics (MD) simulations of biological systems will require an adequate description[unreadable] of these electrostatic forces.[unreadable] [unreadable] To establish a scheme where accuracy of the computation can be controlled systematically, we[unreadable] have proposed a new formulation where the surface charge distribution is used explicitly as[unreadable] a new variable. The surface charge method has a number of advantages. First, it simplifies the[unreadable] boundary conditions from two to one when solving the electrostatics problem; second, it reduces[unreadable] the number of degrees of freedom needed in the calculations; and third, it is applicable to arbitrary[unreadable] geometrical shapes.