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Entropy and Thermodynamics in Biomolecular Simulation
Abstract
Thermodynamics is one of the best established notions in science. Some recent work in biomolecular modeling has sacrificed its rigor in favor of trendy empirical methods. Even in cases where physicsbased energy functions are used, entropy is forgotten or left “for later versions”. This text gives an overview of the utility of a more rigorous treatment of thermodynamics at the molecular level in order to understand protein folding and receptor-ligand binding. An intuitive understanding of thermodynamics is conveyed: enthalpy is the quantity of energy, while entropy stands for its quality. Recent advances in entropy estimation from information theory and physical chemistry are outlined as they apply to biological thermodynamics. The different enthalpic, entropic, and kinetic driving forces behind protein folding and binding are detailed. Finally, some medical applications enabled by an understanding of the free energy folding funnel concept are outlined, such as HIV-1 protease folding inhibitors.
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