Physical Foundation of Biomolecular Interactions

National Library Of Medicine

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Abstract

Biomolecular interactions determine how transcription[unreadable] factors recognize their DNA binding[unreadable] sites, how proteins interact with each other, and[unreadable] consequently how a biological system functions.[unreadable] Since many biological molecules bear considerable[unreadable] electric charge, electrostatic interactions are[unreadable] among the most important when studying biomolecular[unreadable] interactions. However, electrostatic[unreadable] interactions in biological systems are difficult[unreadable] to calculate accurately in practice. Aside from[unreadable] the significants charges carried by biomolecules[unreadable] such as DNA and proteins, the solvent itself [unreadable] namely, water produces considerable electrostatic[unreadable] effects. Furthermore, hydrogen bonds, known to[unreadable] be involved in helix formation in both DNA and[unreadable] proteins, are essentially electrostatic in origin.[unreadable] Indeed, it seems that electrostatic effects often[unreadable] drive the physical-chemical processes in biological[unreadable] systems and, thereby, determine biological[unreadable] function. Therefore, any attempt to perform[unreadable] molecular dynamics (MD) simulations of biological[unreadable] systems will require an adequate description[unreadable] of these electrostatic forces.[unreadable] [unreadable] In the past, we developed a controllable scheme for computing the electrostatic energy.[unreadable] In principle, one may take the numerical derivative to obtain the electrostatic force.[unreadable] In reality, the numerical derivative computations are expensive and may become even more[unreadable] expensive when a high degree of accuracy is demanded. In order to have a practical system for[unreadable] simulation of biomolecular systems, it becomes necessary to calculate the electrostatic forces[unreadable] by function evaluation of analytical formulae, which is the primary effort of this [unreadable] fiscal year. In the process of doing this, we have also implemented a more stable method for [unreadable] evaluating mathematical functions in a rotated coordinate system.